Skip to content

chore: Update the Galaxy wrappers #1465

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
pavanvidem wants to merge 25 commits into
base: master
Choose a base branch
from
Open

chore: Update the Galaxy wrappers #1465

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
25 commits
Select commit Hold shift + click to select a range
73069e4
Add Docker container requirement for deepTools
pavanvidem Sep 8, 2026
32f83d1
Update deeptools requirement in deepTools_macros.xml
pavanvidem Sep 8, 2026
59af6ef
testing an obsolete param
pavanvidem Sep 9, 2026
e651df5
use *_old binaries
pavanvidem Sep 9, 2026
93704d1
revert old binary usage
pavanvidem Sep 10, 2026
aff01a6
remove --ignoreDuplicates from bamCoverage, bamCompare, multiBamSumma…
pavanvidem Sep 10, 2026
09c0032
Remove --exactScaling entirely
pavanvidem Sep 10, 2026
094bf3f
Remove SES option for --scaleFactorsMethod, --sampleLength and --numb…
pavanvidem Sep 10, 2026
2e6b71e
Remove plotly inputs and outputs everywhere
pavanvidem Sep 10, 2026
e48dc0f
Remove --plotTitle from bigwigCompare
pavanvidem Sep 10, 2026
2f95e16
add --no_collapse option and include it in tests
pavanvidem Sep 10, 2026
d3ade57
add --sortUsingSamples to computeMatrix
pavanvidem Sep 10, 2026
3a832f3
add --chromosomesToSkip and a test to multiBigwigSummary
pavanvidem Sep 10, 2026
eec5492
add --fixedStep param and a test to bigwigCompare
pavanvidem Sep 10, 2026
e093d10
add --boxAroundHeatmaps param and a test to plotHeatmap
pavanvidem Sep 10, 2026
12756f9
add fixedStep commandline
pavanvidem Sep 10, 2026
6924c72
add --ggplot param
pavanvidem Sep 10, 2026
6a37ab8
add --interpolationMethod to plotHeatmap
pavanvidem Sep 10, 2026
db0cec3
add --clusterUsingSamples to plotHeatmap and plotProfiler
pavanvidem Sep 10, 2026
be71e73
add --refPointLabel to plotProfiler and remove conditional
pavanvidem Sep 10, 2026
d39586f
add --labels --addLabels to plotPCA and plotProfile
pavanvidem Sep 10, 2026
3c907ad
add --transcriptID --transcript_id_designator to computeMatrixOperations
pavanvidem Sep 10, 2026
4f0b3e7
Use correct param defaults
pavanvidem Sep 10, 2026
bd65c15
remove duplicate use of params in plotEnrichment
pavanvidem Sep 10, 2026
a520f4a
simplify and merge common params into macros
pavanvidem Sep 10, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
53 changes: 17 additions & 36 deletions galaxy/wrapper/bamCompare.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,11 +30,7 @@

--binSize $binSize

#if $scaling.method == 'SES':
--scaleFactorsMethod SES
--sampleLength $scaling.sampleLength
--numberOfSamples $scaling.numberOfSamples
#elif $scaling.method == 'readCount':
#if $scaling.method == 'readCount':
--scaleFactorsMethod readCount
#elif $scaling.method == 'own':
--scaleFactors '$scaling.scaleFactor1:$scaling.scaleFactor2'
Expand All @@ -46,7 +42,6 @@
#end if

--operation $comparison.type
$exactScaling

#if $comparison.type in ['ratio','log2']:
--pseudocount $comparison.pseudocount
Expand All @@ -62,6 +57,7 @@
#end if

@ADVANCED_OPTS_READ_PROCESSING@
$advancedOpt.no_collapse
$advancedOpt.skipNAs
$advancedOpt.skipZeroOverZero

Expand All @@ -84,17 +80,9 @@
<param name="method" type="select"
label="Method to use for scaling the largest sample to the smallest">
<option value="readCount" selected="true">read count</option>
<option value="SES">signal extraction scaling (SES), check with plotFingerprint before using it!</option>
<option value="own">enter own scaling factors</option>
<option value="None">Don't scale reads. Samples can instead be normalized using one of the normalization methods</option>
</param>
<when value="SES">
<param argument="--sampleLength" type="integer" value="1000" min="10"
label="Length in bases used to sample the genome and compute the size or scaling factors."
help="The default is fine. Only change it if you know what you are doing."/>
<param argument="--numberOfSamples" type="integer" value="100000" min="0"
label="Number of samplings taken from the genome to compute the scaling factors"/>
</when>
<when value="readCount"/>
<when value="own">
<expand macro="scaleFactors"/>
Expand Down Expand Up @@ -142,34 +130,26 @@
</when>
</conditional>

<expand macro="exactScaling"/>
<param name="outFileFormat" type="select" label="Coverage file format">
<option value="bigwig" selected="true">bigwig</option>
<option value="bedgraph">bedgraph</option>
</param>
<expand macro="region_limit_operation"/>
<conditional name="advancedOpt">
<param name="showAdvancedOpt" type="select" label="Show advanced options" >
<option value="no" selected="true">no</option>
<option value="yes">yes</option>
</param>
<when value="no"/>
<when value="yes">
<expand macro="smoothLength"/>
<expand macro="read_processing_options"/>

<expand macro="skipNAs"/>
<expand macro="skipZeroOverZero"/>
<expand macro="advancedOpt_scaffold">
<expand macro="smoothLength"/>
<expand macro="read_processing_options"/>
<expand macro="no_collapse"/>
<expand macro="skipNAs"/>
<expand macro="skipZeroOverZero"/>

<param argument="--ignoreForNormalization" type="text" value="" size="50"
label="regions that should be excluded for calculating the scaling factor"
help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor.
For example, if you know of copy number variations between samples then you may want to exclude these.
Another typical example is the difference in chromosome X copies between males and females in many species.
Example inputs are chrX,chrY,chr3 or chr10:12220-128932"/>
<expand macro="blacklist"/>
</when>
</conditional>
<param argument="--ignoreForNormalization" type="text" value="" size="50"
label="regions that should be excluded for calculating the scaling factor"
help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor.
For example, if you know of copy number variations between samples then you may want to exclude these.
Another typical example is the difference in chromosome X copies between males and females in many species.
Example inputs are chrX,chrY,chr3 or chr10:12220-128932"/>
<expand macro="blacklist"/>
</expand>
</inputs>
<outputs>
<data format="bigwig" name="outFileName">
Expand Down Expand Up @@ -235,6 +215,7 @@
<param name="showAdvancedOpt" value="yes"/>
<param name="outFileFormat" value="bedgraph"/>
<param name="binSize" value="10"/>
<param name="no_collapse" value="false"/>
<param name="type" value="ratio"/>
<param name="pseudocount" value="1 1"/>
<output name="outFileName" ftype="bedgraph">
Expand Down
89 changes: 40 additions & 49 deletions galaxy/wrapper/bamCoverage.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,6 @@
#if str($region).strip() != '':
--region '$region'
#end if
$exactScaling

#if $advancedOpt.showAdvancedOpt == "yes":
#if str($advancedOpt.scaleFactor).strip() != '':
Expand Down Expand Up @@ -96,58 +95,50 @@
<option value="bigwig" selected="true">bigwig</option>
<option value="bedgraph">bedgraph</option>
</param>
<expand macro="exactScaling"/>
<expand macro="region_limit_operation"/>

<conditional name="advancedOpt">
<param name="showAdvancedOpt" type="select" label="Show advanced options" >
<expand macro="advancedOpt_scaffold">
<expand macro="scaleFactor"/>
<expand macro="smoothLength"/>

<param argument="ignoreForNormalization" type="text" value=""
label="Regions that should be excluded for normalization"
help="A list of chromosome names separated by spaces
containing those chromosomes that should be excluded
during normalization. This is useful when
considering samples with unequal coverage across
chromosomes, like male and female samples. Example: chrX chrM"/>

<expand macro="skipNAs"/>
<expand macro="read_processing_options"/>

<param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
label="Determine nucleosome positions from MNase-seq data"
help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data. By default, only fragments between 130 and 200 bases will be used, though this can be changed with the --minFragmentLength and --maxFragmentLength options."/>

<param argument="--Offset" type="text" value="" optional="True"
label="Offset inside each alignment to use for the signal location."
help="Uses this offset inside of each read as the signal. This is useful in
cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
should be used to denote where the signal is (rather than the span of the
whole alignment). This can be paired with the --filterRNAstrand option. Note
that negative values indicate offsets from the end of each read. A value of
1 indicates the first base of the alignment (taking alignment orientation
into account). Likewise, a value of -1 is the last base of the alignment. An
offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
used to specify a range of positions. Note that specifying something like
--Offset 5 -1 will result in the 5th through last position being used, which
is equivalent to trimming 4 bases from the 5-prime end of alignments."/>

<param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand."
help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
<option value="no" selected="true">no</option>
<option value="yes">yes</option>
<option value="forward">forward</option>
<option value="reverse">reverse</option>
</param>
<when value="no"/>
<when value="yes">
<expand macro="scaleFactor"/>
<expand macro="smoothLength"/>

<param argument="ignoreForNormalization" type="text" value=""
label="Regions that should be excluded for normalization"
help="A list of chromosome names separated by spaces
containing those chromosomes that should be excluded
during normalization. This is useful when
considering samples with unequal coverage across
chromosomes, like male and female samples. Example: chrX chrM"/>

<expand macro="skipNAs"/>
<expand macro="read_processing_options"/>

<param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
label="Determine nucleosome positions from MNase-seq data"
help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data. By default, only fragments between 130 and 200 bases will be used, though this can be changed with the --minFragmentLength and --maxFragmentLength options."/>

<param argument="--Offset" type="text" value="" optional="True"
label="Offset inside each alignment to use for the signal location."
help="Uses this offset inside of each read as the signal. This is useful in
cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
should be used to denote where the signal is (rather than the span of the
whole alignment). This can be paired with the --filterRNAstrand option. Note
that negative values indicate offsets from the end of each read. A value of
1 indicates the first base of the alignment (taking alignment orientation
into account). Likewise, a value of -1 is the last base of the alignment. An
offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
used to specify a range of positions. Note that specifying something like
--Offset 5 -1 will result in the 5th through last position being used, which
is equivalent to trimming 4 bases from the 5-prime end of alignments."/>

<param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand."
help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
<option value="no" selected="true">no</option>
<option value="forward">forward</option>
<option value="reverse">reverse</option>
</param>
<expand macro="blacklist"/>
</when>
</conditional>
<expand macro="blacklist"/>
</expand>
</inputs>
<outputs>
<data format="bigwig" name="outFileName">
Expand Down
48 changes: 20 additions & 28 deletions galaxy/wrapper/bamPEFragmentSize.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
#if $advancedOpt.outRawFragmentLengths
--outRawFragmentLengths '$fragLengths'
#end if
$advancedOpt.ggplot
#end if
> '$outfile'
]]>
Expand All @@ -53,33 +54,25 @@
</sanitizer>
</param>
<expand macro="plotTitle"/>
<conditional name="advancedOpt">
<param name="showAdvancedOpt" type="select" label="Show advanced options">
<option value="no" selected="true">no</option>
<option value="yes">yes</option>
</param>
<when value="no"/>
<when value="yes">
<param argument="--binSize" type="integer" value="1000" min="1" optional="true"
label="bin size, in bases" help="Length in bases of the window used to sample the genome. (--binSize)"/>
<param argument="--distanceBetweenBins" type="integer" value="1000000" min="0" optional="true"
label="bin spacing, in bases"
help="To reduce the computation time, not every possible genomic bin is sampled. This option allows you to set the distance between bins actually sampled from. Larger numbers are sufficient for high coverage samples, while smaller values are useful for lower coverage samples. Note that if you specify a value that results in too few (&lt;1000) reads sampled, the value will be decreased. (--distanceBetweenBins)"/>
<param argument="--table" type="boolean" truevalue="--table" falsevalue=""
label="Write metrics to a tab-separated file?"
help="Write the read/fragment metrics to a tab-separated file, which is primarily useful for more automated downstream processing."/>
<param argument="--outRawFragmentLengths" type="boolean" truevalue="--outRawFragmentLengths" falsevalue=""
label="Write a file containing the read/fragment length information?"
help="Write the read/fragment length distribution underlying the (optional) plot to a file. This can then be processed in R or other downstream applications."/>
<param argument="--logScale" type="boolean" truevalue="--logScale" falsevalue=""
label="Plot log frequencies"
help="Plot the frequencies on the log10 scale"/>
<param argument="--maxFragmentLength" type="integer" min="0" value="0"
label="Maximum fragment length"
help="Maximum fragment length included in the histogram. A value of 0 (the default) denotes twice the mean fragment length"/>
<expand macro="blacklist"/>
</when>
</conditional>
<expand macro="advancedOpt_scaffold">
<param argument="--binSize" type="integer" value="1000" min="1" optional="true"
label="bin size, in bases" help="Length in bases of the window used to sample the genome. (--binSize)"/>
<expand macro="distanceBetweenBins" DISTANCE="1000000"/>
<param argument="--table" type="boolean" truevalue="--table" falsevalue=""
label="Write metrics to a tab-separated file?"
help="Write the read/fragment metrics to a tab-separated file, which is primarily useful for more automated downstream processing."/>
<param argument="--outRawFragmentLengths" type="boolean" truevalue="--outRawFragmentLengths" falsevalue=""
label="Write a file containing the read/fragment length information?"
help="Write the read/fragment length distribution underlying the (optional) plot to a file. This can then be processed in R or other downstream applications."/>
<param argument="--logScale" type="boolean" truevalue="--logScale" falsevalue=""
label="Plot log frequencies"
help="Plot the frequencies on the log10 scale"/>
<param argument="--maxFragmentLength" type="integer" min="0" value="0"
label="Maximum fragment length"
help="Maximum fragment length included in the histogram. A value of 0 (the default) denotes twice the mean fragment length"/>
<expand macro="blacklist"/>
<expand macro="ggplot" />
</expand>

</inputs>
<outputs>
Expand All @@ -90,7 +83,6 @@
<when input="outFileFormat" value="pdf" format="pdf"/>
<when input="outFileFormat" value="svg" format="svg"/>
<when input="outFileFormat" value="eps" format="eps"/>
<when input="outFileFormat" value="plotly" format="html"/>
</change_format>
</data>
<data name="table" format="tabular" label="${tool.name} on ${on_string}: Read/Fragment metrics in tabular format">
Expand Down
23 changes: 8 additions & 15 deletions galaxy/wrapper/bigwigAverage.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -38,22 +38,15 @@
<option value="bedgraph">bedgraph</option>
</param>
<expand macro="region_limit_operation"/>
<conditional name="advancedOpt">
<param name="showAdvancedOpt" type="select" label="Show advanced options">
<option value="no" selected="true">no</option>
<option value="yes">yes</option>
</param>
<when value="no"/>
<when value="yes">
<param argument="--binSize" type="integer" value="50" min="1"
label="Length, in bases, of the non-overlapping bins used for averaging the score over the regions length"
help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>
<expand macro="advancedOpt_scaffold">
<param argument="--binSize" type="integer" value="50" min="1"
label="Length, in bases, of the non-overlapping bins used for averaging the score over the regions length"
help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>

<expand macro="skipNAs"/>
<param name="scaleFactors" type="text" value="1" label="Scale factors (one per bigwig separated by ':')"/>
<expand macro="blacklist"/>
</when>
</conditional>
<expand macro="skipNAs"/>
<param name="scaleFactors" type="text" value="1" label="Scale factors (one per bigwig separated by ':')"/>
<expand macro="blacklist"/>
</expand>
</inputs>
<outputs>
<data format="bigwig" name="outFileName">
Expand Down
Loading
Loading