| Previous changeset 2:ea3fc1adee75 (2015-11-11) Next changeset 4:4d343c1f606b (2019-12-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01 |
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modified:
bamtools.xml |
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removed:
tool_dependencies.xml |
| b |
| diff -r ea3fc1adee75 -r 04866f817daa bamtools.xml --- a/bamtools.xml Wed Nov 11 12:33:26 2015 -0500 +++ b/bamtools.xml Wed Jan 18 11:47:11 2017 -0500 |
| b |
| b'@@ -1,232 +1,193 @@\n <?xml version="1.0"?>\n-<tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.2">\n- <description>BAM datasets and perform other transformations</description>\n- <requirements>\n- <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>\n- <requirement type="package" version="0.1.18">samtools</requirement>\n- </requirements>\n-\n- <command>\n- ##set up input files\n-\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-\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-\n- ##finished setting up inputs\n-\n- ##start bamtools commandline\n-\n- bamtools\n-\n- #if str( $analysis_type.analysis_type_selector ) == "convert":\n-\n- convert\n-\n- -format ${analysis_type.format_type.format_type_selector}\n-\n- #if str( $analysis_type.format_type.format_type_selector ) == "pileup":\n-\n- ${analysis_type.format_type.mapqual}\n- -fasta "${reference_fasta_filename}"\n-\n- #elif str( $analysis_type.format_type.format_type_selector ) == "sam":\n-\n- ${analysis_type.format_type.noheader}\n-\n- #end if\n-\n- -out $out_file1\n-\n- #elif str( $analysis_type.analysis_type_selector ) == "count":\n-\n- count\n- > $out_file1\n-\n- #elif str( $analysis_type.analysis_type_selector ) == "coverage":\n-\n- coverage\n- -out $out_file1\n-\n- #elif str( $analysis_type.analysis_type_selector ) == "header":\n-\n- header\n- > $out_file1\n-\n- #elif str( $analysis_type.analysis_type_selector ) == "merge":\n-\n- merge\n- -out $out_file1\n-\n- #elif str( $analysis_type.analysis_type_selector ) == "random":\n-\n- random\n- -n ${analysis_type.count}\n- -seed ${analysis_type.seed}\n- -out $out_file1\n-\n- #elif str( $analysis_type.analysis_type_selector ) == "revert":\n-\n- revert\n- ${analysis_type.keepDuplicate}\n- ${analysis_type.keepQualities}\n- -out $out_file1\n-\n- #elif str( $analysis_type.analysis_type_selector ) == "sort":\n-\n- sort\n- ${analysis_type.byname}\n- -out $out_file1\n-\n- #end if\n-\n- #for $bam_count, $input_bam in enumerate( $input_bams ):\n- -in "localbam_${bam_count}.bam"\n- #end for\n-\n-\n- </command>\n- <inputs>\n-\n- <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>\n-\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- <option value="count">Count</option>\n- <option value="coverage">Coverage</option>\n- <option value="header">Header</option>\n- <option value="merge">Merge</option>\n- <option value="random">Random</option>\n- <option value="revert">Revert</option>\n- <!-- The sort option below is commented out as BAM files in Galaxy are reference sorted by dafault. -->\n- <!-- Allowing users for sort files may break donstream functionality. -->\n- <!-- To enable sort option simply uncomment the line below: -->\n- <!-- <option value="sort">Sort</option> -->\n- </param>\n- '..b'mat_type_selector" value="bed" format="bed" />\n+ <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" />\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="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+ <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />\n+ <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />\n+ </change_format>\n+ </data>\n </outputs>\n <tests>\n- <test>\n- <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>\n- <param name="analysis_type_selector" value="convert"/>\n- <param name="format_type_selector" value="pileup"/>\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- </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- </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- </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- </test>\n+ <test>\n+ <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>\n+ <param name="analysis_type_selector" value="convert"/>\n+ <param name="format_type_selector" value="pileup"/>\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+ </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+ </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+ </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+ </test>\n </tests>\n-\n- <stdio>\n- <exit_code range="1:" />\n- </stdio>\n-\n- <help>\n+ <help>\n \n **What is does**\n \n@@ -284,8 +245,8 @@\n \n Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki\n \n- </help>\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btr174</citation>\n- </citations>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btr174</citation>\n+ </citations>\n </tool>\n' |
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| diff -r ea3fc1adee75 -r 04866f817daa tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 11 12:33:26 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bamtools" version="2.3.0_2d7685d2ae"> - <repository changeset_revision="7d6da4982f19" name="package_bamtools_2_3_0_2d7685d2ae" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="0.1.18"> - <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |