Mercurial > repos > padge > clipkit

changeset 4:770695339600 draft default tip

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"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
author padge
date Mon, 11 Apr 2022 13:08:12 +0000
parents 34f21474cdea
children
files clipkit.xml
diffstat 1 files changed, 32 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/clipkit.xml	Fri Mar 25 17:35:03 2022 +0000
+++ b/clipkit.xml	Mon Apr 11 13:08:12 2022 +0000
@@ -41,39 +41,65 @@
         <param name="complement" type="boolean" truevalue="--complement" falsevalue="" checked="False" label="create complement of the trimmed alignment" />
     </inputs>
     <outputs>
-        <data name="trimmed_output" format="fasta" label="Trimmed alignment."/>
+        <data name="trimmed_output" format="fasta" label="Trimmed alignment.">
+            <!-- <filter>out_format_selector == 'fasta'</filter> -->
+            <change_format>
+                <when input="out_format_selector" value="fasta" format="fasta" />
+                <when input="out_format_selector" value="clustal" format="clustal" />
+                <when input="out_format_selector" value="maf" format="maf" />
+                <when input="out_format_selector" value="mauve" format="xmfa" />
+                <when input="out_format_selector" value="stockholm" format="stockholm" />
+                <when input="out_format_selector" value="phylip" format="phylip" />
+                <when input="out_format_selector" value="phylip_sequential" format="phylip" />
+                <when input="out_format_selector" value="phylip_relaxed" format="phylip" />
+            </change_format>
+        </data>
         <data name="log_output" format="txt" label="Clipkit log."/>
         <data name="complement_output" format="fasta" label="Clipkit complement.">
             <filter>complement</filter>
+            <change_format>
+                <when input="out_format_selector" value="fasta" format="fasta" />
+                <when input="out_format_selector" value="clustal" format="clustal" />
+                <when input="out_format_selector" value="maf" format="maf" />
+                <when input="out_format_selector" value="mauve" format="xmfa" />
+                <when input="out_format_selector" value="stockholm" format="stockholm" />
+                <when input="out_format_selector" value="phylip" format="phylip" />
+                <when input="out_format_selector" value="phylip_sequential" format="phylip" />
+                <when input="out_format_selector" value="phylip_relaxed" format="phylip" />
+            </change_format>
         </data>
     </outputs>
     <tests>
         <test>
             <param name="input1" value="simple.fa"/>
             <param name="mode_selector" value="smart-gap" />
+            <param name="out_format_selector" value="fasta" />
             <param name="gaps" value="0.9" />
-            <output name="trimmed_output" file="simple.fa.clipkit"/>
+            <output name="trimmed_output" file="simple.fa.clipkit" ftype="fasta"/>
             <output name="log_output" file="simple.fa.clipkit.log"/>
         </test>
         <test>
             <param name="input1" value="simple.fa"/>
             <param name="mode_selector" value="gappy" />
+            <param name="out_format_selector" value="fasta" />
             <param name="gaps" value="0.2" />
-            <output name="trimmed_output" file="gappy.simple.fa.clipkit"/>
+            <output name="trimmed_output" file="gappy.simple.fa.clipkit" ftype="fasta"/>
         </test>
         <test>
             <param name="input1" value="simple.fa"/>
             <param name="mode_selector" value="gappy" />
+            <param name="out_format_selector" value="fasta" />
             <param name="gaps" value="0.2" />
-            <output name="trimmed_output" file="gappy.simple.fa.clipkit"/>
+            <output name="trimmed_output" file="gappy.simple.fa.clipkit" ftype="fasta"/>
             <output name="log_output" file="gappy.simple.fa.clipkit.log"/>
         </test>
         <test>
             <param name="input1" value="simple.fa"/>
             <param name="mode_selector" value="kpi" />
             <param name="complement" value="true" />
+            <param name="out_format_selector" value="fasta" />
             <param name="gaps" value="0.9" />
-            <output name="trimmed_output" file="kpi.simple.fa.clipkit"/>
+            <output name="trimmed_output" file="kpi.simple.fa.clipkit" ftype="fasta"/>
             <output name="complement_output" file="kpi.simple.fa.clipkit.complement"/>
         </test>
         <test>
@@ -81,7 +107,7 @@
             <param name="mode_selector" value="kpi-gappy" />
             <param name="out_format_selector" value="phylip_relaxed" />
             <param name="gaps" value="0.7" />
-            <output name="trimmed_output" file="of.gaps.simple.phylip_relaxed"/>
+            <output name="trimmed_output" file="of.gaps.simple.phylip_relaxed" ftype="phylip"/>
             <output name="log_output" file="of.gaps.simple.phylip_relaxed.log"/>
         </test>
     </tests>