Mercurial > repos > bgruening > suspenders
diff suspenders.xml @ 0:35b4ff47bf09 draft
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author | bgruening |
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date | Sat, 02 Aug 2014 11:18:24 -0400 |
parents | |
children | 7a5fa8282f82 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/suspenders.xml Sat Aug 02 11:18:24 2014 -0400 @@ -0,0 +1,95 @@ +<?xml version="1.0"?> +<tool name="suspenders" id="bg_suspenders" version="0.2.5.0"> + <description>merging of labeled alignments</description> + <requirements> + <requirement type="package" version="0.2.5">suspenders</requirement> + <requirement type="package" version="1.2.1">matplotlib</requirement> + <requirement type="package" version="0.7.7">pysam</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + <command> +<![CDATA[ + #set $inputs = "" + #for $counter, $input_bam in enumerate( $reference_source.input_bams ): + ln -s "${input_bam.input_bam}" "${counter}.bam"; + ln -s "${input_bam.input_bam.metadata.bam_index}" "${counter}.bai"; + set $inputs += '%s ' % $counter + #end for + + pysuspenders + $labels + $union + $quality + $pileup + $image + $mate_all + $union_all + $random_filter + #if $chart: + -c $image + #end if + -p \${GALAXY_SLOTS:-4} + $output + $inputs +]]> + </command> + <inputs> + <repeat name="input_bams" title="BAM files" min="2" help="sorted by read name"> + <param name="input_bam" type="data" format="bam" label="BAM file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> + </param> + </repeat> + + <param name="labels" type="boolean" truevalue="--lapels" falsevalue="--normal-input" + checked="True" + label="Input has lapels tags" help="--lapels/--normal-input" /> + + <param name="union" type="boolean" truevalue="--union" falsevalue="" + label="Merge the files using the union filter" help="--union"/> + + <param name="quality" type="boolean" truevalue="--quality" falsevalue="" + checked="True" label="Merge the files using the quality filter" help="--quality"/> + + <param name="pileup" type="boolean" truevalue="--pileup" falsevalue="" + label="merge the files using the quality filter, then the pileup height filter" help="--pileup"/> + + <param name="chart" type="boolean" truevalue="True" falsevalue="False" + label="save pileup chart to an image" help=""/> + + <param name="mate_all" type="boolean" truevalue="--mate-all" falsevalue="" + label="compare unmated segments to mated ones" help="--mate-all"/> + + <param name="union_all" type="boolean" truevalue="--union-all" falsevalue="" + label="Use union filter if other filters fail" help="always active for --union (--union-all)"/> + + <param name="random_filter" type="boolean" truevalue="--random-filer" falsevalue="" + label="Use random filter if other filters fail" help="default for --quality and --pileup (--random-filter)"/> + + </inputs> + <outputs> + <data name="output" format="bam" label="${tool.name} on ${on_string}"/> + <data name="image" format="png" label="${tool.name} on ${on_string}: Chart"> + <filter>chart is True</filter> + <data> + </outputs> + <tests> + + </tests> + <help> +<![CDATA[ + +**What it does** + +Allows the merging of alignments that have been annotated using pylapels into a single alignment that picks the highest quality alignment. + +https://pypi.python.org/pypi/suspenders/ + +]]> +</help> +</tool>