diff duplex.xml @ 0:d2e46adc199e draft

planemo upload commit 35b743e6492923c0e2b1e5e434eaf4e56d268108

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/duplex.xml	Mon Nov 23 22:06:21 2015 -0500
@@ -0,0 +1,61 @@
+<?xml version="1.0"?>
+<tool id="duplex" name="Make consensus reads" version="0.1">
+  <description>from duplex sequencing data</description>
+  <requirements>
+    <requirement type="package" version="0.1">duplex</requirement>
+    <requirement type="set_environment">DUPLEX_DIR</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+    python \$DUPLEX_DIR/duplex.py -r $min_reads -q $qual_thres -F $qual_format $input
+    #if $keep_sscs:
+      --sscs-file $sscs
+    #end if
+    > duplex.fa
+    && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=1 duplex.fa > $output1
+    && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=2 duplex.fa > $output2
+  ]]>
+  </command>
+  <inputs>
+    <param name="input" type="data" format="tabular" label="Aligned input reads" />
+    <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
+    <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/>
+    <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+">
+      <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>
+      <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
+    </param>
+    <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences" />
+  </inputs>
+  <outputs>
+    <data name="output1" format="fasta" label="$tool.name on $on_string (mate 1)"/>
+    <data name="output2" format="fasta" label="$tool.name on $on_string (mate 2)"/>
+    <data name="sscs" format="fasta" label="$tool.name on $on_string (SSCS)">
+      <filter>keep_sscs</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="families.msa.tsv"/>
+      <output name="output1" file="families.cons_1.fa"/>
+      <output name="output2" file="families.cons_2.fa"/>
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families.
+
+-----
+
+**Input**
+
+This expects the output format of the "Align families" tool.
+
+-----
+
+**Output**
+
+This will output final, duplex consensus reads in two FASTA files (first and second reads in the pairs). Optionally, you can save the single-strand reads too, in a separate FASTA file.
+
+    </help>
+</tool>