diff tools/mothur/chop.seqs.xml @ 0:ee4fee239fe7 draft default tip

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mothur/chop.seqs.xml	Fri Jun 03 09:32:47 2016 -0400
@@ -0,0 +1,74 @@
+<tool profile="16.07" id="mothur_chop_seqs" name="Chop.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Trim sequences to a specified length</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        echo 'chop.seqs(
+            fasta=$fasta,
+            numbases=$numbases,
+            keep=$keep,
+            countgaps=$countgaps,
+            short=$short,
+            #if $name:
+                name=$name,
+            #end if
+            #if $group:
+                group=$group,
+            #end if
+            #if $count:
+                count=$count,
+            #end if
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur &&
+
+        ## move output files to correct destination
+        prefix="$fasta" &&
+        mv mothur.*.logfile "$logfile" &&
+        mv \${prefix%.dat}*.chop.fasta "$out_fasta"
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to be chopped"/>
+        <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/>
+        <param name="keep" type="select" label="keep - Part of the sequence to keep">
+            <option value="front">front</option>
+            <option value="back">back</option>
+        </param>
+        <param name="countgaps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="countgaps - Count gaps as bases"/>
+        <param name="short" type="boolean" truevalue="true" falsevalue="false" checked="false" label="short - keep sequences that are too short to chop"/>
+        <param name="name" type="data" format="name" label="name file" optional="true"/>
+        <param name="group" type="data" format="group" label="group file" optional="true"/>
+        <param name="count" type="data" format="mothur.count_table" label="count file" optional="true"/>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
+        <data name="out_fasta" format_source="fasta" label="${tool.name} on ${on_string}: chop.fasta"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
+            <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names"/>
+            <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta" compare="contains"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The chop.seqs_ command reads a fasta file of sequences and outputs a .chop.fasta file containing the trimmed sequences. It works on both aligned and unaligned sequences.
+
+.. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs
+
+v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>