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Update MAF to interval to use job working directory instead of __new_file_path__.

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Daniel Blankenberg
2014-04-18 12:34:08 -04:00
parent 5739c37cbf
commit 213986aa7f
1 changed files with 1 additions and 1 deletions
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tools/maf/maf_to_interval.xml
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@@ -1,6 +1,6 @@
<tool id="MAF_To_Interval1" name="MAF to Interval" force_history_refresh="True">
<description>Converts a MAF formatted file to the Interval format</description>
<command interpreter="python">maf_to_interval.py $input1 $out_file1 $out_file1.id $__new_file_path__ $input1.dbkey $species $input1.metadata.species $complete_blocks $remove_gaps</command>
<command interpreter="python">maf_to_interval.py "${ input1 }" "${ out_file1 }" "${ out_file1.id }" "." "${ input1.dbkey }" "${ species }" "${ input1.metadata.species }" "${ complete_blocks }" "${ remove_gaps }"</command>
<inputs>
<param format="maf" name="input1" type="data" label="MAF file to convert"/>
<param name="species" type="select" label="Select additional species" display="checkboxes" multiple="true" help="The species matching the dbkey of the alignment is always included. A separate history item will be created for each species.">