| Previous changeset 1:a548b3c6ed00 (2015-02-11) Next changeset 3:ba685c655e18 (2015-02-11) |
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Commit message:
final upload |
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modified:
annotate_variants.xml bamsort.xml cloudmap.xml convert.xml covstats.xml deletion_predictor.xml fileinfo.xml reheader.xml sam_header.xml snap_caller.xml snp_caller_caller.xml snpeff_genomes.xml varextract.xml vcf_filter.xml |
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added:
toolshed_macros.xml |
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| diff -r a548b3c6ed00 -r 72d20758ba2c annotate_variants.xml --- a/annotate_variants.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/annotate_variants.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="annotate_variants" name="Variant Annotation"> <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd annotate |
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| diff -r a548b3c6ed00 -r 72d20758ba2c bamsort.xml --- a/bamsort.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/bamsort.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="bamsort" name="Sort BAM file"> <description>Sort a BAM file by coordinates (or names) of the mapped reads</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd sort "$inputfile" -o "$output" --oformat $oformat $by_name |
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| diff -r a548b3c6ed00 -r 72d20758ba2c cloudmap.xml --- a/cloudmap.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/cloudmap.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="cloudmap_prepare" name="Prepare variant data for mapping"> <description>with the CloudMap series of tools.</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd cloudmap "$ifile" ${run.mode} |
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| diff -r a548b3c6ed00 -r 72d20758ba2c convert.xml --- a/convert.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/convert.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="convert" name="Convert"> <description>between different sequence data formats</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd convert |
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| diff -r a548b3c6ed00 -r 72d20758ba2c covstats.xml --- a/covstats.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/covstats.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="coverage_stats" name="Coverage Statistics"> <description>Calculate coverage statistics for a BCF file as generated by the Variant Calling tool</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd covstats "$ifile" --ofile "$output_vcf" |
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| diff -r a548b3c6ed00 -r 72d20758ba2c deletion_predictor.xml --- a/deletion_predictor.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/deletion_predictor.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="deletion_prediction" name="Deletion Prediction for paired-end data"> <description>Predicts deletions in one or more aligned read samples based on coverage of the reference genome and on insert sizes</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd delcall |
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| diff -r a548b3c6ed00 -r 72d20758ba2c fileinfo.xml --- a/fileinfo.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/fileinfo.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="fileinfo" name="Retrieve File Information"> <description>for supported data formats.</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd info "$ifile" -o "$outputfile" --verbose --oformat $oformat |
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| diff -r a548b3c6ed00 -r 72d20758ba2c reheader.xml --- a/reheader.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/reheader.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,9 +1,10 @@ <tool id="reheader" name="Reheader BAM file"> <description>From a BAM file generate a new file with the original header (if any) replaced or modified by that found in a second SAM file</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore": |
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| diff -r a548b3c6ed00 -r 72d20758ba2c sam_header.xml --- a/sam_header.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/sam_header.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="ngs_run_annotation" name="NGS Run Annotation"> <description>Create a SAM format header from run metadata for sample annotation.</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd header |
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| diff -r a548b3c6ed00 -r 72d20758ba2c snap_caller.xml --- a/snap_caller.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/snap_caller.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="read_alignment" name="SNAP Read Alignment"> <description>Map sequence reads to a reference genome using SNAP</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd snap-batch -s |
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| diff -r a548b3c6ed00 -r 72d20758ba2c snp_caller_caller.xml --- a/snp_caller_caller.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/snp_caller_caller.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="variant_calling" name="Variant Calling"> <description>From a reference and aligned reads generate a BCF file with position-specific variant likelihoods and coverage information</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd varcall |
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| diff -r a548b3c6ed00 -r 72d20758ba2c snpeff_genomes.xml --- a/snpeff_genomes.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/snpeff_genomes.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="snpeff_genomes" name="List Installed SnpEff Genomes"> <description>Checks the local SnpEff installation to compile a list of currently installed genomes</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd snpeff-genomes -o "$outputfile" |
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| diff -r a548b3c6ed00 -r 72d20758ba2c toolshed_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolshed_macros.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -0,0 +1,7 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.1.5.2">mimodd</requirement> + </requirements> + </xml> +</macros> |
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| diff -r a548b3c6ed00 -r 72d20758ba2c varextract.xml --- a/varextract.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/varextract.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="extract_variants" name="Extract Variant Sites"> <description>from a BCF file</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd varextract "$ifile" |
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| diff -r a548b3c6ed00 -r 72d20758ba2c vcf_filter.xml --- a/vcf_filter.xml Wed Feb 11 08:57:11 2015 -0500 +++ b/vcf_filter.xml Wed Feb 11 09:23:43 2015 -0500 |
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| @@ -1,8 +1,9 @@ <tool id="vcf_filter" name="VCF Filter"> <description>Extracts lines from a vcf variant file based on field-specific filters</description> - <requirements> - <requirement type="package">mimodd</requirement> - </requirements> + <macros> + <import>toolshed_macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> mimodd vcf-filter |