Mercurial > repos > iuc > intervene
changeset 3:21beb30956c2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit f0241966e9185e5960947d12dcb490cce1fc6301
| author | iuc |
|---|---|
| date | Fri, 21 Oct 2022 16:07:46 +0000 |
| parents | 33b8c5eedc04 |
| children | |
| files | intervene_pairwise.xml intervene_upset.xml macros.xml test-data/bed_pairwise_fisher.pdf |
| diffstat | 4 files changed, 38 insertions(+), 12 deletions(-) [+] |
line wrap: on
line diff
--- a/intervene_pairwise.xml Wed Aug 10 08:23:43 2022 +0000 +++ b/intervene_pairwise.xml Fri Oct 21 16:07:46 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@+galaxy1"> +<tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>and heatmap for genomic intervals</description> <xrefs> <xref type="bio.tools">intervene</xref> @@ -17,7 +17,10 @@ --type $type --input #echo " ".join(["'%s'" % file for file in $input]) --names $labels ---compute $compute +--compute $compute_conditional.compute +#if $compute_conditional.compute == 'fisher' + --genome '$compute_conditional.genome' +#end if #if str($corrtype) != 'None' --corr --corrtype $corrtype @@ -35,15 +38,28 @@ ]]></command> <inputs> <param argument="--input" type="data" format="interval" multiple="true" label="Select input files for which to produce intersections"/> - <param argument="--compute" type="select" label="Use this metric for the heatmap"> - <option value="count">count: calculates the number of overlaps</option> - <option value="frac" selected="true">frac: calculates the fraction of overlap</option> - <option value="jaccard">jaccard: calculate the Jaccard statistic</option> - <option value="reldist">reldist: calculate the distribution of relative distances</option> - <!-- fisher option needs additional genome assembly, probably triggers on demand download - <option value="fisher">fisher: calculate Fisher`s statistic</option> - --> - </param> + <conditional name="compute_conditional"> + <param argument="--compute" type="select" label="Use this metric for the heatmap"> + <option value="count">count: calculates the number of overlaps</option> + <option value="frac" selected="true">frac: calculates the fraction of overlap</option> + <option value="jaccard">jaccard: calculate the Jaccard statistic</option> + <option value="reldist">reldist: calculate the distribution of relative distances</option> + <option value="fisher">fisher: calculate Fisher`s statistic</option> + </param> + <when value="count"/> + <when value="frac"/> + <when value="jaccard"/> + <when value="reldist"/> + <when value="fisher"> + <param argument="--genome" type="text" value="" label="Reference genome ID" help="Needs to be a string assembly name such as mm10 or hg38"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z]+</validator> + </param> + </when> + </conditional> <param argument="--corrtype" type="select" label="Select the type of correlation"> <option value="None">Don't calculate correlation</option> <option value="pearson">Pearson correlation</option> @@ -92,6 +108,15 @@ <output name="plot" value="bed_pairwise.pdf" compare="sim_size"/> <output name="matrix" value="matrix.txt" /> </test> + <!-- Test fisher option --> + <test expect_num_outputs="1"> + <param name="input" value="a.bed,b.bed,c.bed"/> + <conditional name="compute_conditional"> + <param name="compute" value="fisher"/> + <param name="genome" value="mm10"/> + </conditional> + <output name="plot" value="bed_pairwise_fisher.pdf" compare="sim_size"/> + </test> </tests> <help><![CDATA[ **What it does**
--- a/intervene_upset.xml Wed Aug 10 08:23:43 2022 +0000 +++ b/intervene_upset.xml Fri Oct 21 16:07:46 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="intervene_upset" name="UpSet diagram" version="@TOOL_VERSION@"> +<tool id="intervene_upset" name="UpSet diagram" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>of intersection of genomic regions or list sets</description> <xrefs> <xref type="bio.tools">intervene</xref>
--- a/macros.xml Wed Aug 10 08:23:43 2022 +0000 +++ b/macros.xml Fri Oct 21 16:07:46 2022 +0000 @@ -31,5 +31,6 @@ </citations> </xml> <token name="@TOOL_VERSION@">0.6.5</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@ESCAPE_IDENTIFIER@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token> </macros>