Mercurial > repos > yutaka-saito > bsfcall
diff bsfcall_wrapper.xml @ 1:20930a8f700b
rename some files
author | yutaka-saito |
---|---|
date | Sun, 19 Apr 2015 22:39:26 +0900 |
parents | bsf-call_wrapper.xml@06f8460885ff |
children | f274c166e738 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bsfcall_wrapper.xml Sun Apr 19 22:39:26 2015 +0900 @@ -0,0 +1,116 @@ +<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). +-->