diff orthogroups_tool.xml @ 4:427dd144d915 draft

planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9

--- a/orthogroups_tool.xml	Fri Jan 19 09:51:12 2018 -0500
+++ b/orthogroups_tool.xml	Tue Feb 27 08:42:05 2018 -0500
@@ -18,7 +18,7 @@
     <![CDATA[        
         #set $infiles = ""
         #for $input in $inputs_fasta
-            ln -s '$input' '$input.element_identifier';
+            ln -s '$input' '$input.element_identifier'.fasta;
             #set $infiles = $infiles + $input.element_identifier + ","
         #end for
         #set $infiles = $infiles[:-1]
@@ -26,10 +26,10 @@
         $__tool_directory__/scripts/format_transdecoder_headers.sh '$orthogroups' tmp_orthogroups.txt
         &&
         python $__tool_directory__/scripts/filter_orthofinder.py tmp_orthogroups.txt $nbspec $nbseq               
-        #if '$verbosity':
+        #if $verbosity=="T":
             -v
         #end if
-        #if '$paralogs':
+        #if $paralogs=="T":
             -p
         #end if
 
@@ -42,8 +42,8 @@
         <param name="inputs_fasta" type="data" format="fasta" multiple="true" label="Outputs from Filter Assemblies" help="Contains the nucleic sequences to retrieve."/>
         <param name="nbspec" type="integer" value="0" label="Number of studied species" help="Specifies the TOTAL (no less) number of species of the analysis"/>
         <param name="nbseq" type="integer" value="3" label="Minimal number of sequences per orthogroup" help="Drop orthogroups with less than x sequences :" />
-        <param name="verbosity" type="boolean" label="verbosity" help="Turn on this paramater to display an additional summary table (computed before the pralogous filtering)" />
-        <param name="paralogs" type="boolean" label="paralogs" help="Turn on this parameter to obtain an additional output (orthogroups files before paralogous filtering)" />
+        <param name="verbosity" type="boolean" checked="True" truevalue="T" falsevalue="F" label="verbosity" help="Turn on this paramater to display an additional summary table (computed before the pralogous filtering)" />
+        <param name="paralogs" type="boolean" checked="False" truevalue="T" falsevalue="F" label="paralogs" help="Turn on this parameter to obtain an additional output (orthogroups files before paralogous filtering)" />
     </inputs>
 
     <outputs>
@@ -85,6 +85,24 @@
                 <element name="orthogroup_7_2_sequences_withParalogs" value="orthogroups_withParalogs/orthogroup_7_2_sequences_withParalogs.fasta" />
             </output_collection>
         </test>
+        <test>
+            <param name="orthogroups" value="Orthogroups.txt"/>
+            <param name="inputs_fasta" value="output_filterassemblies/AcAcaud_trinity.fasta,output_filterassemblies/AmAmphi_trinity.fasta,output_filterassemblies/ApApomp_trinity.fasta,output_filterassemblies/AsAsp1_trinity.fasta"/>
+            <param name="nbspec" value="4"/>
+            <param name="nbseq" value="2"/>
+            <param name="verbosity" value="True"/>
+            <param name="paralogs" value="False"/>
+            <output name="output" value="2_orthogroups_tool.output" lines_diff="2"/>
+            <output_collection name="orthogroups_fasta" type="list">
+                <element name="orthogroup_1_3_sequences" value="filtered_orthogroups/orthogroup_1_3_sequences.fasta" />
+                <element name="orthogroup_2_4_sequences" value="filtered_orthogroups/orthogroup_2_4_sequences.fasta" />
+                <element name="orthogroup_3_2_sequences" value="filtered_orthogroups/orthogroup_3_2_sequences.fasta" />
+                <element name="orthogroup_4_3_sequences" value="filtered_orthogroups/orthogroup_4_3_sequences.fasta" />
+                <element name="orthogroup_5_3_sequences" value="filtered_orthogroups/orthogroup_5_3_sequences.fasta" />
+                <element name="orthogroup_6_3_sequences" value="filtered_orthogroups/orthogroup_6_3_sequences.fasta" />
+                <element name="orthogroup_7_2_sequences" value="filtered_orthogroups/orthogroup_7_2_sequences.fasta" />
+            </output_collection>
+        </test>
     </tests>
 
     <help>