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Update cummeRbund to retrieve genes and samples from input metadata. #506

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Update cummeRbund to retrieve genes and samples from input metadata. #506

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27 changes: 15 additions & 12 deletions tools/cummerbund/cummeRbund.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="cummeRbund" name="cummeRbund" version="2.16.0">
<tool id="cummeRbund" name="cummeRbund" version="2.16.0+galaxy1" profile="18.09">
<description>visualize Cuffdiff output</description>
<macros>
<import>cummeRbund_macros.xml</import>
Expand All @@ -8,7 +8,6 @@
<requirement type="package" version="1.0.1">r-argparse</requirement>
<requirement type="package" version="2.16.0">bioconductor-cummerbund</requirement>
</requirements>
<code file="cummeRbund_options.py"/>
<command detect_errors="aggressive">
<![CDATA[
#for i, p in enumerate($plots):
Expand All @@ -22,7 +21,8 @@
#if $p.plot.multiple_genes.multiple_genes_selector == "yes":
--features $p.plot.multiple_genes.features --gene_selector
#for gene in $p.plot.multiple_genes.genes:
--genes ${gene.gene_id}
#set $gene_id = str($gene.gene_id).split(': ')[0]
--genes $gene_id
#end for
#end if
#elif $p.plot.type == "maplot":
Expand All @@ -32,29 +32,33 @@
#if $p.plot.multiple_genes.multiple_genes_selector == "yes":
--features $p.plot.multiple_genes.features --gene_selector
#for gene in $p.plot.multiple_genes.genes:
--genes ${gene.gene_id}
#set $gene_id = str($gene.gene_id).split(': ')[0]
--genes $gene_id
#end for
#end if
#elif $p.plot.type == "heatmap":
--clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10
#if len($p.plot.genes) > 0:
--gene_selector
#for gene in $p.plot.genes:
--genes ${gene.gene_id}
#set $gene_id = str($gene.gene_id).split(': ')[0]
--genes $gene_id
#end for
#end if
#elif $p.plot.type == "cluster":
--features $p.plot.features --k $p.plot.k --iter_max $p.plot.iter_max
#if len($p.plot.genes) > 0:
#for gene in $p.plot.genes:
--genes ${gene.gene_id}
#set $gene_id = str($gene.gene_id).split(': ')[0]
--genes $gene_id
#end for
#end if
#elif $p.plot.type in [ "expressionplot", "expressionbarplot" ]:
#if $p.plot.type == "expressionplot":
$p.plot.draw_summary
#end if
--features $p.plot.features $p.plot.error_bars --genes ${p.plot.gene_id} $p.plot.replicates $p.plot.log10
#set $gene_id = str($p.plot.gene_id).split(': ')[0]
--features $p.plot.features $p.plot.error_bars --genes $gene_id $p.plot.replicates $p.plot.log10
#end if
#if $p.plot.type == "density":
$p.plot.log10
Expand All @@ -63,7 +67,7 @@
#end for
]]></command>
<inputs>
<param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
<param name="input_database" type="data" format="cuffdiff.sqlite" label="Select backend database (sqlite)" />
<repeat name="plots" title="Plots">
<param name="width" type="integer" value="1280" label="The width of the image"/>
<param name="height" type="integer" value="960" label="The height of the image"/>
Expand Down Expand Up @@ -109,8 +113,7 @@
<expand macro="multiple_genes_conditional" />
</when>
<when value="volcano">
<param name="x" type="select" label="First sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
<param name="y" type="select" label="Second sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
<expand macro="xy_selector" />
<expand macro="multiple_genes_conditional" />
</when>
<when value="heatmap">
Expand Down Expand Up @@ -142,15 +145,15 @@
<when value="scatterMatrix" />
<when value="expressionplot">
<expand macro="features_selector" />
<param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
<expand macro="gene_selector" />
<param name="draw_summary" type="boolean" truevalue="--summary" falsevalue="" checked="False" label="Draw a 'summary' line with mean FPKM values for each condition?"/>
<param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
<expand macro="replicates_checkbox" />
<expand macro="log10_checkbox" />
</when>
<when value="expressionbarplot">
<expand macro="features_selector" />
<param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
<expand macro="gene_selector" />
<param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
<expand macro="replicates_checkbox" />
<expand macro="log10_checkbox" />
Expand Down
25 changes: 22 additions & 3 deletions tools/cummerbund/cummeRbund_macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,33 @@
<macro name="log10_checkbox">
<param name="log10" type="boolean" truevalue="--log10" falsevalue="" checked="True" label="Apply log10 transformation on FPKM values?"/>
</macro>
<macro name="samples_meta">
<options>
<filter type="data_meta" ref="input_database" key="samples" />
</options>
</macro>
<macro name="genes_meta">
<options>
<filter type="data_meta" ref="input_database" key="genes" />
</options>
</macro>
<macro name="gene_selector">
<param name="gene_id" type="select" label="Gene ID">
<expand macro="genes_meta" />
</param>
</macro>
<macro name="xy_selector">
<param name="x" type="select" label="Sample name for x axis" dynamic_options="get_samples(input_database.dataset.file_name)" />
<param name="y" type="select" label="Sample name for y axis" dynamic_options="get_samples(input_database.dataset.file_name)" />
<param name="x" type="select" label="Sample name for x axis">
<expand macro="samples_meta" />
</param>
<param name="y" type="select" label="Sample name for y axis">
<expand macro="samples_meta" />
</param>
</macro>
<macro name="genes_selector">
<repeat name="genes" title="Genes" min="2">
<!-- Cannot create a heatmap for less than two genes -->
<param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
<expand macro="gene_selector" />
</repeat>
</macro>
<macro name="features_selector">
Expand Down
11 changes: 0 additions & 11 deletions tools/cummerbund/cummeRbund_options.py
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