diff clipkit.xml @ 2:e9cf321ee7be draft

"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"

--- a/clipkit.xml	Fri Mar 25 13:05:29 2022 +0000
+++ b/clipkit.xml	Fri Mar 25 17:33:41 2022 +0000
@@ -3,7 +3,7 @@
         <requirement type="package" version="1.3">clipkit</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[    
-        clipkit $input1 -m ${mode_selector} -o $trimmed_output --log ${complement}
+        clipkit $input1 -m ${mode_selector} -o $trimmed_output -of $out_format_selector --log ${complement} 
         #if $gaps
             --gaps ${gaps}
         #end if;
@@ -27,6 +27,16 @@
             <option value="kpi-smart-gap">kpi-smart-gap</option>
             <option value="kpi-gappy">kpi-gappy</option>
         </param>
+        <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list">
+            <option value="fasta">FASTA format</option>
+            <option value="clustal">CLUSTAL format</option>
+            <option value="maf">MAF format</option>
+            <option value="mauve">MAUVE format</option>
+            <option value="stockholm">STOCKHOLM format</option>
+            <option value="phylip">PHYLIP/PHYLIP4 format</option>
+            <option value="phylip_sequential">PHYLIP/PHYLIP4 sequential format</option>
+            <option value="phylip_relaxed">PHYLIP/PHYLIP4 relaxed format</option>
+        </param>
         <param name="gaps" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="gappyness" help="Specify gappyness threshold (between 0 and 1). Default: 0.9" multiple="false"/>
         <param name="complement" type="boolean" truevalue="--complement" falsevalue="" checked="False" label="create complement of the trimmed alignment" />
     </inputs>
@@ -66,6 +76,14 @@
             <output name="trimmed_output" file="kpi.simple.fa.clipkit"/>
             <output name="complement_output" file="kpi.simple.fa.clipkit.complement"/>
         </test>
+        <test>
+            <param name="input1" value="simple.fa"/>
+            <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="log_output" file="of.gaps.simple.phylip_relaxed.log"/>
+        </test>
     </tests>
     <help><![CDATA[         
 Modes
@@ -103,10 +121,10 @@
     ]]></help>
     <citations>
         <citation type="bibtex">
-@misc{githubPhyKIT,
+@misc{githubClipKIT,
   author = {LastTODO, FirstTODO},
   year = {TODO},
-  title = {PhyKIT},
+  title = {ClipKIT},
   publisher = {GitHub},
   journal = {GitHub repository},
   url = {https://github.com/jlsteenwyk/clipkit},