Mercurial > repos > bgruening > deeptools_bigwig_compare
diff deepTools_macros.xml @ 10:163f2951146c draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
author | bgruening |
---|---|
date | Mon, 05 Dec 2016 08:06:20 -0500 |
parents | 5b2abee3aff3 |
children | f90c8a697ee9 |
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--- a/deepTools_macros.xml Tue Oct 25 19:04:47 2016 -0400 +++ b/deepTools_macros.xml Mon Dec 05 08:06:20 2016 -0500 @@ -98,11 +98,11 @@ </xml> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.3.6</token> + <token name="@WRAPPER_VERSION@">2.4.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.7.10">python</requirement> - <requirement type="package" version="2.3.6">deepTools</requirement> + <requirement type="package" version="2.4.1">deeptools</requirement> <yield /> </requirements> <expand macro="stdio" /> @@ -285,11 +285,21 @@ </param> </xml> + <xml name="sortRegionsComputeMatrix"> + <param argument="--sortRegions" type="select" label="Sort regions" + help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> + <option value="no">no ordering</option> + <option value="keep" selected="true">maintain the same ordering as the input files</option> + <option value="descend">descending order</option> + <option value="ascend">ascending order</option> + </param> + </xml> + <xml name="sortRegions"> <param argument="--sortRegions" type="select" label="Sort regions" help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> <option value="no">no ordering</option> - <option value="descend" selected="true">descending order</option> + <option value="descend">descending order</option> <option value="ascend">ascending order</option> </param> </xml> @@ -362,21 +372,62 @@ </xml> <xml name="multiple_input_bams"> - <param argument="--bamfiles" type="data" format="bam" min="1" - label="Bam file" multiple="true" - help=""/> + <conditional name="multibam_conditional"> + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"> + <param argument="--bamfiles" type="data" format="bam" min="1" + label="Bam file" multiple="true" + help=""/> + </when> + <when value="Yes"> + <repeat name="multibam_repeats" min="1" title="BAM Files"> + <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> + </repeat> + </when> + </conditional> </xml> <xml name="multiple_input_bams_min2"> - <param argument="--bamfiles" type="data" format="bam" min="2" - label="Bam file" multiple="true" - help=""/> + <conditional name="multibam_conditional"> + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples +is vital to you, select Yes below."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"> + <param argument="--bamfiles" type="data" format="bam" min="2" + label="Bam file" multiple="true" + help=""/> + </when> + <when value="Yes"> + <repeat name="multibam_repeats" min="2" title="BAM Files"> + <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> + </repeat> + </when> + </conditional> </xml> <xml name="multiple_input_bigwigs"> - <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" - label="Bigwig file" - help="A Bigwig file."/> + <conditional name="multibigwig_conditional"> + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples +is vital to you, select Yes below."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"> + <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" + label="Bigwig file" + help="A Bigwig file."/> + </when> + <when value="Yes"> + <repeat name="multibigwig_repeats" min="2" title="BigWig files"> + <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/> + </repeat> + </when> + </conditional> </xml> <xml name="plotTitle"> @@ -390,12 +441,21 @@ <![CDATA[ #set files=[] #set labels=[] - #for $counter, $bamfile in enumerate($bamfiles): - ln -s "${bamfile}" "./${counter}.bam" && - ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && - #silent $files.append('%s.bam' % $counter) - #silent $labels.append("'%s'" % ($bamfile.display_name)) - #end for + #if $multibam_conditional.orderMatters == "No": + #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): + ln -s "${bamfile}" "./${counter}.bam" && + ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && + #silent $files.append('%s.bam' % $counter) + #silent $labels.append("'%s'" % ($bamfile.display_name)) + #end for + #else: + #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): + ln -s "${f.bamfile}" "./${counter}.bam" && + ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" && + #silent $files.append('%s.bam' % $counter) + #silent $labels.append("'%s'" % ($f.bamfile.display_name)) + #end for + #end if ]]> </token> @@ -403,11 +463,19 @@ <![CDATA[ #set files=[] #set labels=[] - #for $counter, $bigwig in enumerate($bigwigfiles): - ln -s "${bigwig}" "${counter}.bw" && - #silent $files.append('%s.bw' % $counter) - #silent $labels.append("'%s'" % ($bigwig.display_name)) - #end for + #if $multibigwig_conditional.orderMatters == "No": + #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): + ln -s "${bigwig}" "${counter}.bw" && + #silent $files.append('%s.bw' % $counter) + #silent $labels.append("'%s'" % ($bigwig.display_name)) + #end for + #else: + #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): + ln -s "${f.bigwig}" "${counter}.bw" && + #silent $files.append('%s.bw' % $counter) + #silent $labels.append("'%s'" % ($f.bigwig.display_name)) + #end for + #end if ]]> </token>