Mercurial > repos > yutaka-saito > bsfcall
view bsfcall_wrapper.xml @ 1:20930a8f700b
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author | yutaka-saito |
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date | Sun, 19 Apr 2015 22:39:26 +0900 |
parents | bsf-call_wrapper.xml@06f8460885ff |
children | f274c166e738 |
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<tool id="bsfcall" name="bsfcall" version="1.0.0"> <description>Mapping bisulfite-seq reads and calling methylated cytosines</description> <!-- <version_command></version_command> --> <requirements> <requirement type="set_environment">TOOLDIR</requirement> </requirements> <command interpreter="perl"> bsfcall_wrapper.pl TOOLDIR $reference.source $read.end \${GALAXY_SLOTS:-1} #if $reference.source=="indexed": $reference.index.fields.path #else if $reference.source=="history": $reference.own_file #else #end if #if $read.end=="single-end" $in #else if $read.end=="paired-end" $in1 $in2 #else #end if </command> <inputs> <conditional name="reference"> <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?"> <option value="indexed">Use a built-in genome index</option> <option value="history">Use a genome from the history and build index</option> </param> <when value="indexed"> <param name="index" type="select" label="Select reference genome"> <options from_data_table="bsfcall_indexes"> <filter type="sort_by" column="2"/> <validator type="no_options" message="No indexes are available for the selected input dataset"/> </options> </param> </when> <when value="history"> <param name="own_file" type="data" format="fasta" label="Select reference genome"/> </when> </conditional> <conditional name="read"> <param name="end" type="select" label="Will you use single-end reads or paired-end reads?"> <option value="single-end">Single-end reads</option> <option value="paired-end">Paired-end reads</option> </param> <when value="single-end"> <param name="in" type="data" format="fastqsanger" label="Single-end reads in fastqsanger format"/> </when> <when value="paired-end"> <param name="in1" type="data" format="fastqsanger" label="Paired-end reads 1 in fastqsanger format"/> <param name="in2" type="data" format="fastqsanger" label="Paired-end reads 2 in fastqsanger format"/> </when> </conditional> </inputs> <outputs> <data name="outres" format="tabular" label="${tool.name} on ${on_string}: result" from_work_dir="bsf-call.out"/> <data name="outlog" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="bsfwork/bsf-call.log"/> </outputs> <help> **bsf-call** Mapping bisulfite-seq reads and calling methylated cytosines ------ **Input format** Inputs are bisulfite-seq reads in fastqsanger format (single-end or paired-end), and a reference genome index (built-in or constructed from your fasta file). ------ **Output format** Output is a six-column tab-delimited file:: Col.| Description ----+-------------------------------------- 1 | chromosome label (e.g. chr1) 2 | genomic position (0-based) 3 | strand (+,-) 4 | mC context (CG, CHG, CHH) 5 | mC rate (float) 6 | read coverage ------ **Contact** Toutai Mituyama mituyama-toutai AT aist.go.jp </help> <citations> <citation type="doi">10.1093/nar/gkt1373</citation> </citations> </tool> <!-- Also note the use of the reserved parameter name GALAXY_DATA_INDEX_DIR - it points to the ~/tool-data directory. \${GALAXY_SLOTS:-4} Number of cores/threads allocated by the job runner or resource manager to the tool for the given job (here 4 is the default number of threads to use if running via custom runner that does not configure GALAXY_SLOTS or in an older Galaxy runtime). -->