diff seqtk_seq.xml @ 0:e0a0fd938de4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_seq.xml	Thu Feb 05 11:52:40 2015 -0500
@@ -0,0 +1,76 @@
+<?xml version="1.0"?>
+<tool id="seqtk_seq" name="seqtk_seq" version="@WRAPPER_VERSION@.0">
+  <description>common transformation of FASTA/Q</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[seqtk seq -q $q
+-X $X
+#if $n and $n != "None" and $n is not None and $n != "":
+-n "$n"
+#end if
+-l $l
+-Q $Q
+-s $s
+-f $f
+#if $M and $M != "None" and $M is not None and $M != "":
+-M "$M"
+#end if
+-L $L
+$c
+$r
+$A
+$C
+$N
+$x1
+$x2
+$V
+
+$in_file
+> $default]]></command>
+  <inputs>
+    <expand macro="in_faq"/>
+    <param label="mask bases with quality lower than INT" help="(-q)" name="q" type="integer" value="0"/>
+    <param label="mask bases with quality higher than INT" help="(-X)" name="X" type="integer" value="255"/>
+    <param area="false" default="0" label="masked bases converted to CHAR; 0 for lowercase" help="(-n)" name="n" type="text"/>
+    <param label="number of residues per line; 0 for 2^32-1" help="(-l)" name="l" type="integer" value="0"/>
+    <param label="quality shift: ASCII-INT gives base quality" help="(-Q)" name="Q" type="integer" value="33"/>
+    <param label="random seed" help="effective with -f (-s)" name="s" type="integer" value="11"/>
+    <param label="sample fraction of sequences" help="(-f)" name="f" type="float" value="1"/>
+    <param area="false" default="null" label="mask regions in BED or name list FILE" help="(-M)" name="M" type="text"/>
+    <param label="drop sequences with length shorter than INT" help="(-L)" name="L" type="integer" value="0"/>
+    <param checked="false" label="mask complement region" help="effective with -M (-c)" name="c" type="boolean" falsevalue="" truevalue="-c"/>
+    <param checked="false" label="reverse complement" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/>
+    <param checked="false" label="force FASTA output (discard quality)" help="(-A)" name="A" type="boolean" falsevalue="" truevalue="-A"/>
+    <param checked="false" label="drop comments at the header lines" help="(-C)" name="C" type="boolean" falsevalue="" truevalue="-C"/>
+    <param checked="false" label="drop sequences containing ambiguous bases" help="(-N)" name="N" type="boolean" falsevalue="" truevalue="-N"/>
+    <param checked="false" label="output the 2n-1 reads only" help="(-1)" name="x1" type="boolean" falsevalue="" truevalue="-1"/>
+    <param checked="false" label="output the 2n reads only" help="(-2)" name="x2" type="boolean" falsevalue="" truevalue="-2"/>
+    <param checked="false" label="shift quality by '(-Q) - 33' " help="(-V)" name="V" type="boolean" falsevalue="" truevalue="-V"/>
+  </inputs>
+  <outputs>
+    <data format_source="in_file" hidden="false" name="default"/>
+  </outputs>
+  <tests>
+    <test>
+      <!-- This is a sorry excuse for a test for a tool which does way more
+           than it should, but upstream decided to put a TON of functionality
+           into a single tool rather than using the single responsibility
+           principle. -->
+      <param name="in_file" value="seqtk_seq.fa"/>
+      <param name="r" value="True"/>
+      <param name="n" value=""/>
+      <param name="M" value=""/>
+      <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Various utilities for transforming FASTA/Q data
+
+@ATTRIBUTION@
+]]></help>
+</tool>