| Previous changeset 3:04866f817daa (2017-01-18) Next changeset 5:befc9dad4ca8 (2021-11-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16" |
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modified:
bamtools.xml |
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added:
macros.xml |
| b |
| diff -r 04866f817daa -r 4d343c1f606b bamtools.xml --- a/bamtools.xml Wed Jan 18 11:47:11 2017 -0500 +++ b/bamtools.xml Wed Dec 04 07:44:35 2019 -0500 |
| [ |
| b'@@ -1,76 +1,69 @@\n <?xml version="1.0"?>\n-<tool id="bamtools" name="Convert, Merge, Randomize" version="2.4.0">\n+<tool id="bamtools" name="Convert, Merge, Randomize" version="@VERSION@.0">\n <description>BAM datasets and perform other transformations</description>\n- <requirements>\n- <requirement type="package" version="2.4.0">bamtools</requirement>\n- <requirement type="package" version="1.3.1">samtools</requirement>\n- </requirements>\n- <stdio>\n- <exit_code range="1:" />\n- </stdio>\n- <command>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command detect_errors="exit_code">\n <![CDATA[\n ##set up input files\n- #for $bam_count, $input_bam in enumerate( $input_bams ):\n- ln -s "${input_bam}" "localbam_${bam_count}.bam" &&\n- ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&\n- #end for\n- #if str( $analysis_type.analysis_type_selector ) == "convert":\n- #if str( $analysis_type.format_type.format_type_selector ) == "pileup":\n- #set $reference_fasta_filename = "localref.fa"\n- #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":\n- ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &&\n- samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for bamtools convert" >&2 &&\n+ ln -s \'${input_bams}\' localbam.bam &&\n+ ln -s \'${input_bams.metadata.bam_index}\' localbam.bam.bai &&\n+ #if str( $analysis_type.analysis_type_selector ) == \'convert\':\n+ #if str( $analysis_type.format_type.format_type_selector ) == \'pileup\':\n+ #set $reference_fasta_filename = \'localref.fa\'\n+ #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == \'history\':\n+ ln -s \'${analysis_type.format_type.reference_source.ref_file}\' \'${reference_fasta_filename}\' &&\n+ samtools faidx \'${reference_fasta_filename}\' 2>&1 || echo \'Error running samtools faidx for bamtools convert\' >&2 &&\n #else:\n #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )\n #end if\n #end if\n #end if\n bamtools\n- #if str( $analysis_type.analysis_type_selector ) == "convert":\n+ #if str( $analysis_type.analysis_type_selector ) == \'convert\':\n convert\n -format ${analysis_type.format_type.format_type_selector}\n- #if str( $analysis_type.format_type.format_type_selector ) == "pileup":\n+ #if str( $analysis_type.format_type.format_type_selector ) == \'pileup\':\n ${analysis_type.format_type.mapqual}\n- -fasta "${reference_fasta_filename}"\n- #elif str( $analysis_type.format_type.format_type_selector ) == "sam":\n+ -fasta \'${reference_fasta_filename}\'\n+ #elif str( $analysis_type.format_type.format_type_selector ) == \'sam\':\n ${analysis_type.format_type.noheader}\n #end if\n- -out $out_file1\n- #elif str( $analysis_type.analysis_type_selector ) == "count":\n+ -out \'$out_file1\'\n+ #elif str( $analysis_type.analysis_type_selector ) == \'count\':\n count\n- > $out_file1\n- #elif str( $analysis_type.analysis_type_selector ) == "coverage":\n+ > \'$out_file1\'\n+ #elif str( $analysis_type.analysis_type_selector ) == \'coverage\':\n coverage\n- -out $out_file1\n- #elif s'..b' == "merge":\n+ > \'$out_file1\'\n+ #elif str( $analysis_type.analysis_type_selector ) == \'merge\':\n merge\n- -out $out_file1\n- #elif str( $analysis_type.analysis_type_selector ) == "random":\n+ -out \'$out_file1\'\n+ #elif str( $analysis_type.analysis_type_selector ) == \'random\':\n random\n -n ${analysis_type.count}\n -seed ${analysis_type.seed}\n- -out $out_file1\n- #elif str( $analysis_type.analysis_type_selector ) == "revert":\n+ -out \'$out_file1\'\n+ #elif str( $analysis_type.analysis_type_selector ) == \'revert\':\n revert\n ${analysis_type.keepDuplicate}\n ${analysis_type.keepQualities}\n- -out $out_file1\n- #elif str( $analysis_type.analysis_type_selector ) == "sort":\n+ -out \'$out_file1\'\n+ #elif str( $analysis_type.analysis_type_selector ) == \'sort\':\n sort\n ${analysis_type.byname}\n- -out $out_file1\n+ -out \'$out_file1\'\n #end if\n- #for $bam_count, $input_bam in enumerate( $input_bams ):\n- -in "localbam_${bam_count}.bam"\n- #end for\n+ -in localbam.bam\n ]]>\n </command>\n <inputs>\n- <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>\n+ <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" />\n <conditional name="analysis_type">\n <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">\n <option value="convert">Convert</option>\n@@ -153,6 +146,7 @@\n <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" />\n <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />\n <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />\n+ <when input="analysis_type.analysis_type_selector" value="count" format="tabular" />\n <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />\n <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />\n <when input="analysis_type.analysis_type_selector" value="random" format="bam" />\n@@ -169,22 +163,22 @@\n <param name="reference_source_selector" value="history" />\n <param name="mapqual" value="true" />\n <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>\n- <output name="output_bam" file="bamtools-convert-pileup.pu" />\n+ <output name="out_file1" file="bamtools-convert-pileup.pu" />\n </test>\n <test>\n <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>\n <param name="analysis_type_selector" value="count"/>\n- <output name="output_bam" file="bamtools-count.tab" />\n+ <output name="out_file1" file="bamtools-count.tab" />\n </test>\n <test>\n <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>\n <param name="analysis_type_selector" value="coverage"/>\n- <output name="output_bam" file="bamtools-coverage.tab" />\n+ <output name="out_file1" file="bamtools-coverage.tab" />\n </test>\n <test>\n <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>\n <param name="analysis_type_selector" value="header"/>\n- <output name="output_bam" file="bamtools-header.txt" />\n+ <output name="out_file1" file="bamtools-header.txt" />\n </test>\n </tests>\n <help>\n' |
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| diff -r 04866f817daa -r 4d343c1f606b macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 04 07:44:35 2019 -0500 |
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| @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<macros> + <token name="@VERSION@">2.4.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">bamtools</requirement> + <requirement type="package" version="1.4.1">samtools</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btr174</citation> + </citations> + </xml> +</macros> \ No newline at end of file |