| Previous changeset 5:8404aa79a631 (2018-05-23) Next changeset 7:d7540a923c7b (2019-12-01) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 6cf009024dfff81b0e0f836b76cf475e7cf84c71 |
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modified:
repeatmasker.xml |
| b |
| diff -r 8404aa79a631 -r 65ab76d58c41 repeatmasker.xml --- a/repeatmasker.xml Wed May 23 14:24:14 2018 -0400 +++ b/repeatmasker.xml Tue Dec 18 14:05:17 2018 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy1" profile="17.01"> +<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy2" profile="17.01"> <description>RepeatMasker</description> <requirements> @@ -6,7 +6,9 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ - RM_LIB_PATH=\$(dirname \$(which RepeatMasker))/../share/RepeatMasker/Libraries && + RM_PATH=\$(which RepeatMasker) && + if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi && + RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries && mkdir lib && export REPEATMASKER_LIB_DIR=\$(pwd)/lib && for file in \$(ls \$RM_LIB_PATH) ; do ln -s \$RM_LIB_PATH/\$file lib/\$file ; done && @@ -189,8 +191,8 @@ <param name="source_type" value="library" /> <param name="repeat_lib" value="repeats.fasta" ftype="fasta" /> <output name="output_masked_genome" file="small.fasta.masked" /> - <output name="output_table" file="small.fasta.stats" lines_diff="2" /> - <output name="output_repeat_catalog" file="small.fasta.cat" /> + <output name="output_table" file="small.fasta.stats" lines_diff="4" /> + <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" /> <output name="output_log" file="small.fasta.log" /> </test> <test expect_num_outputs="7"> @@ -202,8 +204,8 @@ <param name="poly" value="-poly" /> <param name="repeat_lib" value="repeats.fasta" ftype="fasta" /> <output name="output_masked_genome" file="small.fasta.masked" /> - <output name="output_table" file="small.fasta.stats" lines_diff="4" /> - <output name="output_repeat_catalog" file="small.fasta.cat" /> + <output name="output_table" file="small.fasta.stats" lines_diff="6" /> + <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" /> <output name="output_log" file="small.fasta.log" /> <output name="output_alignment" file="small.fasta.align" /> <output name="output_polymorphic" file="small.fasta.poly" /> @@ -217,7 +219,7 @@ <param name="species_list" value="anopheles" /> <output name="output_masked_genome" file="small.fasta.masked" /> <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" /> - <output name="output_repeat_catalog" file="small.fasta.cat" /> + <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" /> <output name="output_log" file="small_repbase.fasta.log" /> </test> </tests> |