Mercurial > repos > morinlab > correct_read_counter

annotate correctReads.xml @ 0:75c4a4c32bae draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 14:18:25 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
1 <tool id="correct_read_counter" name="correctReadCounter" version="1.8.0">
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
2 <description>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
3 Correct Read Counter for GC content and mappability biases
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
4 </description>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
5 <requirements>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
6 <requirement type="binary">Rscript</requirement>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
7 <requirement type="R-module">TitanCNA</requirement>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
8 <requirement type="package" version="3.2.1">R</requirement>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
9 <requirement type="package" version="1.8.0">titancna</requirement>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
10 </requirements>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
11 <command>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
12
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
13 Rscript $__tool_directory__/correctReads.R $tumour $normal $gc $map
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
14 #if $target:
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
15 $target
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
16 #else:
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
17 NULL
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
18 #end if
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
19 $output 2>&amp;1
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
20
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
21 </command>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
22 <inputs>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
23 <param type="data" format="wig" name="normal" label="Normal Read Counts"/>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
24 <param type="data" format="wig" name="tumour" label="Tumour Read Counts"/>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
25 <param type="data" format="wig" name="gc" label="GC Wig"/>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
26 <param type="data" format="wig" name="map" label="MAP Wig"/>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
27 <param type="data" format="txt,bed" name="target" label="Target File" help="Specify Targets if using Exome Data" optional="True"/>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
28 </inputs>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
29 <outputs>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
30 <data format="wig" name="output"/>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
31 </outputs>
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
32 </tool>