| Previous changeset 19:fff3c83ec9b8 (2016-11-28) Next changeset 21:c281993e515b (2016-11-28) |
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Commit message:
Uploaded |
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modified:
shm_csr.xml wrapper.sh |
| b |
| diff -r fff3c83ec9b8 -r ba2511ebd36a shm_csr.xml --- a/shm_csr.xml Mon Nov 28 05:15:16 2016 -0500 +++ b/shm_csr.xml Mon Nov 28 07:23:50 2016 -0500 |
| [ |
| @@ -1,7 +1,7 @@ <tool id="shm_csr" name="SHM & CSR pipeline" version="1.0"> <description></description> <command interpreter="bash"> - wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast + wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast </command> <inputs> <param name="in_file" type="data" label="IMGT zip file to be analysed" /> @@ -71,7 +71,7 @@ <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> </data> - <data format="imgt_archive" name="naive_output_ca" label = "Naive input data from ${in_file.name}" > + <data format="imgt_archive" name="naive_output_all" label = "Naive input data from ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] == "101_101"</filter> </data> |
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| diff -r fff3c83ec9b8 -r ba2511ebd36a wrapper.sh --- a/wrapper.sh Mon Nov 28 05:15:16 2016 -0500 +++ b/wrapper.sh Mon Nov 28 07:23:50 2016 -0500 |
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| @@ -14,10 +14,11 @@ naive_output_cg=${10} naive_output_cm=${11} naive_output_ce=${12} -filter_unique=${13} -class_filter=${14} -empty_region_filter=${15} -fast=${16} +naive_output_all=${13} +filter_unique=${14} +class_filter=${15} +empty_region_filter=${16} +fast=${17} mkdir $outdir tar -xzf $dir/style.tar.gz -C $outdir |