| Previous changeset 12:484e86282f4b (2017-05-15) Next changeset 14:f2e8552cf1d0 (2017-10-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 8991687e2ec5f75d3841c613ea5d8ffda0389654 |
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modified:
rgFastQC.xml |
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| diff -r 484e86282f4b -r 9337dd1fbc66 rgFastQC.xml --- a/rgFastQC.xml Mon May 15 08:34:57 2017 -0400 +++ b/rgFastQC.xml Mon Jun 05 13:49:57 2017 -0400 |
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| @@ -1,22 +1,18 @@ -<tool id="fastqc" name="FastQC" version="0.68"> +<tool id="fastqc" name="FastQC" version="0.69"> <description>Read Quality reports</description> <requirements> <requirement type="package" version="0.11.5">fastqc</requirement> </requirements> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> - <command><![CDATA[ - python '${__tool_directory__}/rgFastQC.py' + <command detect_errors="exit_code"><![CDATA[ + #import re + #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier)) + python '$__tool_directory__/rgFastQC.py' -i '$input_file' - -d '${html_file.files_path}' + -d '$html_file.files_path' -o '$html_file' -t '$text_file' - -f '${input_file.ext}' - -j '${input_file.name}' + -f '$input_file.ext' + -j '$input_name' #if $contaminants.dataset and str($contaminants) > '' -c '$contaminants' #end if |