diff seqtk_mergefa.xml @ 0:e0a0fd938de4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_mergefa.xml	Thu Feb 05 11:52:40 2015 -0500
@@ -0,0 +1,68 @@
+<?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 $q
+$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[
+**What it does**
+
+Merges two fasta files, using ambiguity codes
+
+::
+
+    # seq1.fa
+    >test0
+    ACTGACTGAAA
+
+    # seq2.fa
+    >test0
+    ACTGAMTGCGN
+
+In the following the `-m` option has been set to highlight seqtk-mergefa's features.
+
+::
+
+    >test0
+    ACTGACTGxxa
+
+@ATTRIBUTION@
+]]></help>
+</tool>