diff seqtk_mergefa.xml @ 3:bc7d99f46a5d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d

--- a/seqtk_mergefa.xml	Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_mergefa.xml	Mon Jun 05 13:27:11 2017 -0400
@@ -1,47 +1,48 @@
 <?xml version="1.0"?>
 <tool id="seqtk_mergefa" name="seqtk_mergefa" version="@WRAPPER_VERSION@.0">
-  <description>merge two FASTA/Q files</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk mergefa -q $q
+    <description>merge two FASTA/Q files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+seqtk mergefa
+-q $q
 $i
 $m
 $r
 $h
-
-$in_fa1
-$in_fa2
-
-> $default]]></command>
-  <inputs>
-    <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
-    <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
-    <param label="quality threshold" help="(-q)" name="q" type="integer" value="0"/>
-    <param checked="false" label="take intersection" help="(-i)" name="i" type="boolean" falsevalue="" truevalue="-i"/>
-    <param checked="false" label="convert to lowercase when one of the input base is N" help="(-m)" name="m" type="boolean" falsevalue="" truevalue="-m"/>
-    <param checked="false" label="pick a random allele from het" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/>
-    <param checked="false" label="suppress hets in the input" help="(-h)" name="h" type="boolean" falsevalue="" truevalue="-h"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_fa1" hidden="false" name="default" label="Merger of $in_fa1.name and $in_fa2.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_fa1" value="seqtk_mergefa1.fa"/>
-      <param name="in_fa2" value="seqtk_mergefa2.fa"/>
-      <output name="default" file="seqtk_mergefa.out" ftype="fasta"/>
-    </test>
-    <test>
-      <param name="in_fa1" value="seqtk_mergefa1.fa"/>
-      <param name="in_fa2" value="seqtk_mergefa2.fa"/>
-      <param name="m" value="True" />
-      <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
+'$in_fa1'
+'$in_fa2'
+> '$default'
+    ]]></command>
+    <inputs>
+        <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
+        <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
+        <param argument="-q" type="integer" value="0" label="Quality threshold"/>
+        <param argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Take intersection" />
+        <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Convert to lowercase when one of the input base is N" />
+        <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Pick a random allele from het" />
+        <param argument="-h" type="boolean" truevalue="-h" falsevalue="" checked="false" label="Suppress hets in the input" />
+    </inputs>
+    <outputs>
+        <data name="default" format_source="in_fa1" label="Merger of $in_fa1.name and $in_fa2.name"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_fa1" value="seqtk_mergefa1.fa"/>
+            <param name="in_fa2" value="seqtk_mergefa2.fa"/>
+            <output name="default" file="seqtk_mergefa.out" ftype="fasta"/>
+        </test>
+        <test>
+            <param name="in_fa1" value="seqtk_mergefa1.fa"/>
+            <param name="in_fa2" value="seqtk_mergefa2.fa"/>
+            <param name="m" value="True" />
+            <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Merges two fasta files, using ambiguity codes
@@ -64,6 +65,6 @@
     ACTGACTGxxa
 
 @ATTRIBUTION@
-]]></help>
-  <expand macro="citation" />
+    ]]></help>
+    <expand macro="citation" />
 </tool>