Mercurial > repos > hepcat72 > lumpyexpress

changeset 1:107fa8e0b744 draft

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planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 461cce84aa93505ac05547a2a28865ff8c0dfefb
author hepcat72
date Tue, 16 Oct 2018 17:34:40 -0400
parents e5150e64206a
children bfd745cf84c2
files README.md lumpyexpress.xml
diffstat 2 files changed, 16 insertions(+), 3 deletions(-) [+]
line wrap: on
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Tue Oct 16 17:34:40 2018 -0400
@@ -0,0 +1,11 @@
+# lumpyexpress - a simple wrapper for galaxy
+
+lumpyexpress is a wrapper for lumpy.  This galaxy wrapper includes a shell script which wraps lumpyexpress (and lumpy).  The shell script sorts bam files (if they are not sorted) and indexes bam files (if they are not indexed).  lumpyexpress however only works on paired-end data, therefor, in order to provide simplified processing of split-read data, a simplified call to lumpy with split-read data is made if the data is indicated to be single-end read data (i.e. not paired-end data).
+
+Only required options are used.  Everything else uses the lumpy/lumpyexpress defaults.  If you would like support for additional lumpy/lumpyexpress options, please submit an issue to request it.
+
+lumpy and lumpyexpress were not written by me.  Please refer to the lumpy repository for issues with lumpy itself:
+
+https://github.com/arq5x/lumpy-sv
+
+Issues with this wrapper can be submitted here.
--- a/lumpyexpress.xml	Tue Oct 16 15:55:49 2018 -0400
+++ b/lumpyexpress.xml	Tue Oct 16 17:34:40 2018 -0400
@@ -1,18 +1,18 @@
-<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.0">
+<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.1">
     <description>Single or paired end SV detection</description>
 
     <requirements>
         <requirement type="package" version="2.7">python</requirement>
         <requirement type="package" version="0.8.3">pysam</requirement>
         <requirement type="package" version="1.13.1">numpy</requirement>
-        <requirement type="package" version="0.2.14a">lumpy-sv</requirement>
+        <requirement type="package" version="0.2.13">lumpy-sv</requirement>
         <requirement type="package" version="1.9">samtools</requirement>
         <requirement type="package" version="0.1.24">samblaster</requirement>
         <requirement type="package" version="0.6.5">sambamba</requirement>
         <requirement type="package" version="4.2.1">gawk</requirement>
     </requirements>
 
-    <version_command>___COMMAND___ ___VERSION_FLAG___</version_command>
+    <version_command>lumpy --version</version_command>
 
     <command detect_errors="aggressive">
         <![CDATA[
@@ -64,6 +64,8 @@
             Paired-end data is processed with lumpyexpress using only the required arguments.  Single-end data is processed with lumpy using `-mw 4 -tt 0 -sr id:<SAMPLE>,bam_file:<SAMPLE>.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20`.  Submit an issue to the tool wrapper repo if you would like more options to be available: https://github.com/hepcat72/robs_galaxy_tools
 
             Split reads and discordant reads are extracted from the supplied bam files.  Each bam file should represent a different sample.
+
+            This is a wrapper for lumpyexpress that comes with lumpy-sv version 0.2.13.  The script in the latest version of lumpy-sv (0.2.14a) has some issues when run on galaxy.
         ]]>
     </help>