diff chira_collapse.xml @ 0:872249f5495a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chira_collapse.xml	Sun Jan 19 16:32:04 2020 -0500
@@ -0,0 +1,48 @@
+<tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@0">
+    <description>deduplicate fastq reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />    
+    <command><![CDATA[
+        chira_collapse.py
+        -i '$in'
+        -u '$umi_len'
+        -o '$out'
+    ]]></command>
+
+    <inputs>
+        <param format="fastq" name="in" type="data" label="Input FASTQ file"/>
+        <param name="umi_len" type="integer" value="0"
+               label="Length of the UMI if present at the 5' end of your reads"/>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="out" label="ChiRA collapse FASTQ on ${on_string}"/>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="in" value="reads.fastq" />
+            <output name="out" file="reads.fasta" />
+        </test>
+    </tests>
+
+    <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool deduplicates the reads from the FASTQ file and writes into a fasta each read once with it's read count.
+
+**Inputs**
+
+* Quality and adapter trimmed FASTQ file
+
+**Outputs**
+
+* FASTA file with unique sequences. The headers of the sequence are in the following format: >sequence_id|UMI|read_count
+
+    </help>
+    <expand macro="citations" />
+</tool>