Mercurial > repos > iuc > repmatch_gff3
diff repmatch_gff3.xml @ 4:6acaa2c93f47 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9
| author | iuc |
|---|---|
| date | Wed, 12 Jul 2017 10:11:53 -0400 |
| parents | d7f1312b3455 |
| children | 7cb4c6424ff8 |
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--- a/repmatch_gff3.xml Fri Jan 13 10:52:02 2017 -0500 +++ b/repmatch_gff3.xml Wed Jul 12 10:11:53 2017 -0400 @@ -1,42 +1,34 @@ <?xml version="1.0"?> -<tool id="repmatch_gff3" name="RepMatch" version="@WRAPPER_VERSION@.1"> +<tool id="repmatch_gff3" name="RepMatch" version="@WRAPPER_VERSION@.2"> <description>Match paired peaks from two or more replicates</description> <macros> <import>repmatch_gff3_macros.xml</import> </macros> <expand macro="requirements" /> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range=":-1" /> - <exit_code range="1:" /> - <!-- Check stderr in case the return code has not been set --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> - <command> - python $__tool_directory__/repmatch_gff3.py - #for $i in $input: - --input "${i}" "${i.hid}" - #end for - --method $method - --distance $distance - --replicates $replicates - --output_files $output_files_cond.output_files - --output_matched_peaks "$output_matched_peaks" - #if str($output_files_cond.output_files) in ["all", "matched_peaks_unmatched_peaks"]: - --output_unmatched_peaks "$output_unmatched_peaks" - #end if - #if str($output_files_cond.output_files) =="all": - --output_detail "$output_detail" - --output_statistics_table "$output_statistics_table" - --output_statistics_histogram "$output_statistics_histogram" - #end if - #if str($advanced_options_cond.advanced_options) == "on": - --step $advanced_options_cond.step - --low_limit $advanced_options_cond.low_limit - --up_limit $advanced_options_cond.up_limit - #end if - </command> + <command detect_errors="aggressive"><![CDATA[ +python '$__tool_directory__/repmatch_gff3.py' +#for $i in $input: + --input '${i}' '${i.hid}' +#end for +--method $method +--distance $distance +--replicates $replicates +--output_files $output_files_cond.output_files +--output_matched_peaks '$output_matched_peaks' +#if str($output_files_cond.output_files) in ['all', 'matched_peaks_unmatched_peaks']: + --output_unmatched_peaks '$output_unmatched_peaks' +#end if +#if str($output_files_cond.output_files) == 'all': + --output_detail '$output_detail' + --output_statistics_table '$output_statistics_table' + --output_statistics_histogram '$output_statistics_histogram' +#end if +#if str($advanced_options_cond.advanced_options) == 'on': + --step $advanced_options_cond.step + --low_limit $advanced_options_cond.low_limit + --up_limit $advanced_options_cond.up_limit +#end if + ]]></command> <inputs> <param name="input" type="data" format="gff" multiple="True" min="2" label="Match paired peaks on" /> <param name="method" type="select" label="Method of finding match">