Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

count matrix for edger tool #61

Open
wants to merge 9 commits into
base: master
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from 1 commit
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 4 additions & 0 deletions countmatrixforedger/.shed.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
categories: [Computational chemistry]
description: Additional tools for EDGE-PRO
name: rnaseq_pro_workflow_tools
nsoranzo marked this conversation as resolved.
Show resolved Hide resolved
owner: marpiech
nsoranzo marked this conversation as resolved.
Show resolved Hide resolved
Binary file added countmatrixforedger/RnaSeqInProcaryotes.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
64 changes: 64 additions & 0 deletions countmatrixforedger/countmatrixforedger.xml
Original file line number Diff line number Diff line change
@@ -0,0 +1,64 @@
<tool id="countmatrixforedger" name="countMatrixForEdger" version="1.0">
<description>Make a count matrix for edgeR</description>
nsoranzo marked this conversation as resolved.
Show resolved Hide resolved
<stdio>
<exit_code range="1:" />
</stdio>
<command>
<![CDATA[
#for $i, $s in enumerate( $sample )#
echo -e ${s.sample_data}"\t"${s.sample_name}"\t"${s.sample_group} >> script.data;
#end for#

$__tool_directory__/tools/scrsh.sh script.data;
nsoranzo marked this conversation as resolved.
Show resolved Hide resolved

cat count.matrix > $count_matrix;
cat annotation > $annotation;
cat script.log > $log;
nsoranzo marked this conversation as resolved.
Show resolved Hide resolved
cat error.log > $error_log
nsoranzo marked this conversation as resolved.
Show resolved Hide resolved

]]>
</command>
<inputs>
<repeat name="sample" title="">
<param name="sample_data" type="data" format="data" label="Output matrix from EDGE-pro (out_rpkm)" />
<param name="sample_name" type="text" label="" help="Sample name" />
<param name="sample_group" type="text" label="" help="Sample group name- it has to be the same string for each sample of this group" />
</repeat>
</inputs>
<outputs>
<data name="count_matrix" format="tabular" label="countMatrixForEdger: count matrix"/>
nsoranzo marked this conversation as resolved.
Show resolved Hide resolved
<data name="annotation" format="tabular" label="countMatrixForEdger: annotation"/>
<data name="log" format="txt" label="countMatrixForEdger: log"/>
<data name="error_log" format="txt" label="countMatrixForEdger: error log"/>
</outputs>
<tests>
<test>
<param name="sample_0|sample_data" value="data1" />
<param name="sample_1|sample_data" value="data2" />
<param name="sample_2|sample_data" value="data3" />
<param name="sample_3|sample_data" value="data4" />
<param name="sample_0|sample_name" value="sample1" />
<param name="sample_1|sample_name" value="sample2" />
<param name="sample_2|sample_name" value="sample3" />
<param name="sample_3|sample_name" value="sample4" />
<param name="sample_0|sample_group" value="gr1" />
<param name="sample_1|sample_group" value="gr1" />
<param name="sample_2|sample_group" value="gr2" />
<param name="sample_3|sample_group" value="gr2" />
<output name="count_matrix" file="count.matrix"/>
<output name="annotation" file="annotation"/>
<output name="log" file="script.log"/>
<output name="error_log" file="error.log"/>
</test>

</tests>
<help>
<![CDATA[

nsoranzo marked this conversation as resolved.
Show resolved Hide resolved
]]>
</help>
<citations>
nsoranzo marked this conversation as resolved.
Show resolved Hide resolved
<citation>
</citation>
nsoranzo marked this conversation as resolved.
Show resolved Hide resolved
</citations>
</tool>
Loading