| Previous changeset 14:7563ea7a922d (2023-04-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit 7a5f368a5859e659aa36d0358bb96ca12574e2cc |
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removed:
repeatmasker.xml.orig |
| b |
| diff -r 7563ea7a922d -r ba6d2c32f797 repeatmasker.xml.orig --- a/repeatmasker.xml.orig Mon Apr 24 10:29:31 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,260 +0,0 @@\n-<<<<<<< HEAD\n-<tool id="repeatmasker_wrapper" name="RepeatMasker" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">\n- <description>screen DNA sequences for interspersed repeats and low complexity regions</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro=\'xrefs\'/>\n- <expand macro=\'edam_ontology\' />\n- <expand macro=\'requirements\' />\n- <version_command>repeatmasker --version</version_command>\n- <command detect_errors="exit_code"><![CDATA[\n-=======\n-<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.1.1" profile="17.01">\n- <description>screen DNA sequences for interspersed repeats and low complexity regions</description>\n- <xrefs>\n- <xref type="bio.tools">RepeatMasker</xref>\n- </xrefs>\n- <requirements>\n- <requirement type="package" version="4.1.1">repeatmasker</requirement>\n- </requirements>\n-\n- <command detect_errors="exit_code"><![CDATA[\n->>>>>>> c895e2728 (Update repeatmasker.xml)\n- RM_PATH=\\$(which RepeatMasker) &&\n- if [ -z "\\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\\$PATH)" >&2 ; exit 1 ; fi &&\n-\n- RM_LIB_PATH=\\$(dirname \\$RM_PATH)/../share/RepeatMasker/Libraries &&\n- #if $repeat_source.source_type == "dfam_up":\n- mkdir lib/ &&\n- ln -s \'${repeat_source.dfam_lib}\' lib/RepeatMaskerLib.h5 &&\n- RM_LIB_PATH=\\$(pwd)/lib &&\n- #end if\n-\n- ln -s \'${input_fasta}\' rm_input.fasta &&\n-\n- RepeatMasker -dir \\$(pwd)\n- -libdir \\$RM_LIB_PATH\n- #if $repeat_source.source_type == "library":\n- -lib \'${repeat_source.repeat_lib}\'\n- -cutoff \'${repeat_source.cutoff}\'\n- #else if $repeat_source.source_type == "dfam":\n- #if $repeat_source.species_source.species_from_list == \'yes\':\n- -species $repeat_source.species_source.species_list\n- #else\n- -species \'${repeat_source.species_source.species_name}\'\n- #end if\n- #else if $repeat_source.source_type == "dfam_up":\n- -species \'${repeat_source.species_name}\'\n- #end if\n- -parallel \\${GALAXY_SLOTS:-1}\n- ${gff}\n- ${excln}\n- ${advanced.is_only}\n- ${advanced.is_clip}\n- ${advanced.no_is}\n- ${advanced.rodspec}\n- ${advanced.primspec}\n- ${advanced.nolow}\n- ${advanced.noint}\n- ${advanced.norna}\n- ${advanced.alu}\n- ${advanced.div}\n- ${advanced.search_speed}\n- -frag ${advanced.frag}\n- ## -maxsize ${advanced.maxsize}\n- #if str($advanced.gc):\n- -gc ${advanced.gc}\n- #end if\n- ${advanced.gccalc}\n- ${advanced.nocut}\n- ${advanced.keep_alignments}\n- ${advanced.invert_alignments}\n- ${advanced.xout}\n- ${advanced.xsmall}\n- ${advanced.poly}\n- rm_input.fasta &&\n- #if $advanced.is_only != \'-is_only\':\n- mv rm_input.fasta.masked \'${output_masked_genome}\' &&\n- sed -E \'s/^ *// ; s/ *$//; s/\\+ //; s/ +/\\t/g ; 1,2c SW score\\t% div.\\t% del.\\t% ins.\\tquery sequence\\tpos in query: begin\\tend\\t(left)\\trepeat\\tclass/family\\tpos in repeat: begin\\tend\\t(left)\\tID\' rm_input.fasta.out >\'${output_log}\' &&\n- mv rm_input.fasta.tbl \'${output_table}\' &&\n- #if $gff == \'-gff\':\n- mv rm_input.fasta.out.gff \'${output_gff}\' &&\n- #end if\n- #if $advanced.keep_alignments == \'-ali\':\n- mv rm_input.fasta.align \'${output_alignment}\' &&\n- #end if\n- #if $advanced.poly == \'-poly\':\n- sed -E \'s/^ *// ; s/ *$//; s/\\+ //; s/ +/\\t/g\' rm_input.fasta.polyout >\'${output_polymorphic}\' &&\n- #end if\n- #end if\n- if [ -f \'rm_input.fasta.cat.gz\' ]; then\n- zcat \'rm_input.fasta.cat.gz\' > \'${output_repeat_catalog}\';\n- else\n- mv rm_input.fasta.cat \'${output_repeat_catalog}\';\n- fi\n- ]]>\n- </command>\n-\n- <inputs>\n- <param name="input_fasta" type="data" format="fasta" label="Genomic DNA" />\n- <conditional name="repeat_source">\n- <param label="Repeat library source" name="source_type" type="select" help="To use RepBase, choose \'Custom library of repeats\' and select '..b'g}">\n- <filter>not advanced[\'is_only\'] and gff is True</filter>\n- </data>\n- </outputs>\n- <tests>\n- <test expect_num_outputs="4">\n- <param name="input_fasta" value="small.fasta" ftype="fasta" />\n- <param name="source_type" value="library" />\n- <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />\n- <output name="output_masked_genome" file="small.fasta.masked" />\n- <output name="output_table" file="small.fasta.stats" lines_diff="6" />\n- <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />\n- <output name="output_log" file="small.fasta.log" lines_diff="2"/>\n- </test>\n- <test expect_num_outputs="7">\n- <param name="input_fasta" value="small.fasta" ftype="fasta" />\n- <param name="source_type" value="library" />\n- <param name="gff" value="-gff" />\n- <param name="keep_alignments" value="-ali" />\n- <param name="poly" value="-poly" />\n- <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />\n- <output name="output_masked_genome" file="small.fasta.masked" />\n- <output name="output_table" file="small.fasta.stats" lines_diff="6" />\n- <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />\n- <output name="output_log" file="small.fasta.log" lines_diff="2"/>\n- <output name="output_alignment" file="small.fasta.align" />\n- <output name="output_polymorphic" file="small.fasta.poly" />\n- <output name="output_gff" file="small.fasta.gff" lines_diff="4" />\n- </test>\n- <test expect_num_outputs="4">\n- <param name="input_fasta" value="small.fasta" ftype="fasta" />\n- <param name="source_type" value="dfam" />\n- <param name="species_list" value="human" />\n- <output name="output_masked_genome" file="small_dfam.fasta.masked" />\n- <output name="output_table" file="small_dfam.fasta.stats" lines_diff="2" />\n- <output name="output_repeat_catalog" file="small_dfam.fasta.cat" lines_diff="2" />\n- <output name="output_log" file="small_dfam.fasta.log" lines_diff="2"/>\n- </test>\n- <test expect_num_outputs="4">\n- <param name="input_fasta" value="small.fasta" ftype="fasta" />\n- <param name="source_type" value="dfam_up" />\n- <param name="dfam_lib" value="Dfam_partial_test.h5" ftype="h5" />\n- <param name="species_name" value="rodent" />\n- <output name="output_masked_genome" file="small_dfam_up.fasta.masked" />\n- <output name="output_table" file="small_dfam_up.fasta.stats" lines_diff="2" />\n- <output name="output_repeat_catalog" file="small_dfam_up.fasta.cat" lines_diff="2" />\n- <output name="output_log" file="small_dfam_up.fasta.log" lines_diff="2"/>\n- </test>\n- <test expect_num_outputs="4">\n- <param name="input_fasta" value="small.fasta" ftype="fasta" />\n- <param name="source_type" value="dfam" />\n- <param name="species_list" value="rattus" />\n- <output name="output_masked_genome" file="small_dfam_rattus.fasta.masked" />\n- <output name="output_table" file="small_dfam_rattus.fasta.stats" lines_diff="2" />\n- <output name="output_repeat_catalog" file="small_dfam_rattus.fasta.cat" lines_diff="2" />\n- <output name="output_log" file="small_dfam_rattus.fasta.log" lines_diff="2"/>\n- </test>\n- </tests>\n- <help><![CDATA[\n-RepeatMasker is a program that screens DNA for interspersed repeats and low\n-complexity DNA sequences. The database of repeats to screen for can be\n-provided as a FASTA file or downloaded from RepBase_. If the RepBase option is\n-chosen the RepBaseRepeatMaskerEdition file should be downloaded and\n-unpacked, and the enclosed EMBL format file (\'RMRBSeqs.embl\') should\n-be uploaded to Galaxy for use with this tool.\n-\n-Further documentation is available on the RepeatMasker homepage_.\n-\n-.. _RepBase: http://www.girinst.org/repbase/\n-.. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html\n- ]]>\n- </help>\n- <expand macro="citations" />\n-</tool>\n' |