diff mircounts.xml @ 6:543472c9e272 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577

--- a/mircounts.xml	Tue Sep 05 06:33:16 2017 -0400
+++ b/mircounts.xml	Tue Sep 05 17:54:46 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="mircounts" name="miRcounts" version="1.0.0">
+<tool id="mircounts" name="miRcounts" version="1.1.0">
     <description> Counts miRNA alignments from small RNA sequence data</description>
     <requirements>
         <requirement type="package" version="1.18">gnu-wget</requirement>
@@ -85,6 +85,10 @@
             <option value="2">2</option>
             <option value="3">3</option>
         </param>
+         <param help="Output mature Mir counts" label="Output mature Mir counts"
+             name="output_mir_counts" type="boolean" falsevalue="0" checked="true" truevalue="1" />
+         <param help="Output pre-Mir counts" label="Output pre-Mir counts"
+             name="output_premir_counts" type="boolean" falsevalue="0" checked="true" truevalue="1" />
         <conditional name="plotting">
             <param label="Additional miRNA charts" name="plottingOption" type="select">
                 <option value="no">no</option>
@@ -101,14 +105,16 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="bam" label="BAM alignment" name="output" />
-        <data format="gff3" label="GFF3 generated by miRCounts" name="gff3"/>
+        <data format="bam" label="BAM alignment" name="output" hidden="true" />
+        <data format="gff3" label="GFF3 generated by miRCounts" name="gff3" hidden="true" />
         <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file">
+            <filter>output_premir_counts == True</filter>
             <actions>
                 <action name="column_names" type="metadata" default="Gene,Counts" />
             </actions>
         </data>
         <data format="tabular" label="Mir Counts" name="mir_count_file">
+            <filter>output_mir_counts == True</filter>
             <actions>
                 <action name="column_names" type="metadata" default="Gene,Counts" />
             </actions>
@@ -132,6 +138,8 @@
             <param name="mirbase_version" value="CURRENT"/>
             <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/>
             <param name="plottingOption" value="no"/>
+            <param name="output_premir_counts" value="True"/>
+            <param name="output_mir_counts" value="True"/>
             <output name="output" file="unclipped.out.bam" ftype="bam"/>
             <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/>
             <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
@@ -149,6 +157,8 @@
             <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/>
             <param name="plottingOption" value="yes"/>
             <param name="display" value="relative"/>
+            <param name="output_premir_counts" value="True"/>
+            <param name="output_mir_counts" value="True"/>
             <output name="output" file="unclipped.out.bam" ftype="bam"/>
             <output name="gff3" file="translated_dme.gff3" ftype="gff3"  lines_diff="22"/>
             <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
@@ -164,6 +174,8 @@
             <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/>
             <param name="plottingOption" value="yes"/>
             <param name="display" value="absolute"/>
+            <param name="output_premir_counts" value="True"/>
+            <param name="output_mir_counts" value="True"/>
             <output name="output" file="clipped.out.bam" ftype="bam"/>
             <output name="gff3" file="translated_dme.gff3" ftype="gff3"  lines_diff="22"/>
             <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/>