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changeset 18:44265821f01f draft

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Uploaded
author wrtz
date Thu, 14 Jan 2016 17:51:41 -0500
parents c34371f08c6f
children 8d9aa0763dc1
files samtools_faidx.xml
diffstat 1 files changed, 24 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_faidx.xml	Thu Jan 14 17:51:41 2016 -0500
@@ -0,0 +1,24 @@
+<tool id="samtools_faidx" name="Faidx (SAMtools)" version="1.0.0">
+    <description>Index FASTA file using samtools faidx command</description>
+    <command>
+        ln -s -f $input faidx_in.${input.ext} &amp;&amp;
+
+        samtools faidx
+
+        faidx_in.${input.ext} &amp;&amp;
+        cp faidx_in.${input.ext}.fai $output
+    </command>
+    <inputs>
+        <param name="input" type="data" label="FASTA input file" />
+    </inputs>
+    <outputs>
+        <data name="output" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <help>
+**About this tool**
+
+**Samtools faidx**: Index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. Outputs index of input file.
+
+More info here: http://www.htslib.org/doc/samtools.html
+  </help>
+</tool>
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