Mercurial > repos > dpryan79 > bwameth
diff bwameth.xml @ 20:5924e53ef39c draft default tip
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| author | dpryan79 |
|---|---|
| date | Thu, 15 Sep 2016 04:57:12 -0400 |
| parents | 352e0213806c |
| children |
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--- a/bwameth.xml Wed Sep 14 07:54:59 2016 -0400 +++ b/bwameth.xml Thu Sep 15 04:57:12 2016 -0400 @@ -1,20 +1,11 @@ -<tool id="bwameth" name="bwameth" version="0.20"> - <description>Fast and accurate aligner of BS-Seq reads.</description> - <requirements> - <requirement type="package" version="0.4.6">toolshed</requirement> - <requirement type="package" version="1.2">samtools</requirement> - <requirement type="package" version="0.7.12">bwa</requirement> - <requirement type="package" version="0.20">bwameth</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <regex match="Error:" /> - <regex match="Exception:" /> - <regex match="Exception :" /> - </stdio> - <version_command>bwameth.py --version</version_command> - <command> +<tool id="bwameth" name="bwameth" version="0.2.0.2"> + <description>Fast and accurate aligner of BS-Seq reads.</description> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="0.2.0">bwameth</requirement> + </requirements> + <version_command>bwameth.py --version</version_command> + <command detect_errors="aggressive"> <![CDATA[ #if $referenceSource.source != "indexed": mkdir index_dir && @@ -27,7 +18,7 @@ bwameth.py -t "\${GALAXY_SLOTS:-4}" - --reference ${index} + --reference "${index}" #if str($readGroup).strip() != "": --read-group "${readGroup}" @@ -35,67 +26,93 @@ #if $single_or_paired.single_or_paired_opts == 'single': $single_or_paired.input_singles - #else: + #elif $single_or_paired.single_or_paired_opts == 'paired': $single_or_paired.input_mate1 $single_or_paired.input_mate2 + #else: + $single_or_paired.input_mate1.forward $single_or_paired.input_mate1.reverse #end if - | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" - output + | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -o output.bam - ]]> - </command> - <inputs> - <conditional name="referenceSource"> - <param name="source" type="select" label="Select a genome reference from your history or a built-in index?"> - <option value="history" selected="True">Use one from the history</option> - <option value="indexed">Use a built-in index</option> - </param> - <when value="history"> - <param name="reference" type="data" format="fasta" metadata_name="dbkey" label="Select a genome" help="in FASTA format" /> - </when> - <when value="indexed"> - <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin"> - <options from_data_table="bwameth_indexes"> - <filter type="sort_by" column="2"/> - <validator type="no_options" message="No indexes are available for the selected input dataset"/> - </options> - </param> - </when> - </conditional> + </command> + <inputs> + <conditional name="referenceSource"> + <param name="source" type="select" label="Select a genome reference from your history or a built-in index?"> + <option value="history" selected="True">Use one from the history</option> + <option value="indexed">Use a built-in index</option> + </param> + <when value="history"> + <param name="reference" type="data" format="fasta" metadata_name="dbkey" label="Select a genome" help="in FASTA format" /> + </when> + <when value="indexed"> + <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin"> + <options from_data_table="bwameth_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + </conditional> - <conditional name="single_or_paired"> - <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param name="input_singles" type="data" format="fastq" label="FASTQ" help="FASTQ file." /> - </when> - <when value="paired"> - <param name="input_mate1" type="data" format="fastq" label="First read in pair" help="FASTQ file." /> - <param name="input_mate2" type="data" format="fastq" label="Second read in pair" help="FASTQ file." /> - </when> - </conditional> - <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'"> - <sanitizer sanitize="False"/> - </param> - </inputs> - <outputs> - <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" /> - </outputs> - <tests> - <test> - <param name="referenceSource" value="history" /> - <param name="reference" value="ref.fa.gz" /> - <param name="single_or_paired_opts" value="paired" /> - <param name="input_mate1" value="t_R1.fastq.gz" /> - <param name="input_mate2" value="t_R2.fastq.gz" /> - <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> - </test> - </tests> - <help> + <conditional name="single_or_paired"> + <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + <option value="paired_collection">Paired-end Dataset Collection</option> + </param> + <when value="single"> + <param name="input_singles" type="data" format="fastqsanger" label="FASTQ" help="FASTQ file." /> + </when> + <when value="paired"> + <param name="input_mate1" type="data" format="fastqsanger" label="First read in pair" help="FASTQ file." /> + <param name="input_mate2" type="data" format="fastqsanger" label="Second read in pair" help="FASTQ file." /> + </when> + <when value="paired_collection"> + <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." /> + </when> + </conditional> + <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'"> + <sanitizer sanitize="False"/> + </param> + </inputs> + <outputs> + <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="referenceSource" value="history" /> + <param name="reference" value="ref.fa.gz" /> + <param name="single_or_paired_opts" value="paired" /> + <param name="input_mate1" value="t_R1.fastq.gz" /> + <param name="input_mate2" value="t_R2.fastq.gz" /> + <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> + </test> + <test> + <param name="referenceSource" value="history" /> + <param name="reference" value="ref.fa.gz" /> + <param name="single_or_paired_opts" value="paired_collection" /> + <param name="input_mate1"> + <collection type="paired"> + <element name="forward" value="t_R1.fastq.gz" /> + <element name="reverse" value="t_R2.fastq.gz" /> + </collection> + </param> + <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> + </test> + </tests> + <help> <![CDATA[ **What it does** BWA-meth performs alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. The methodology employed for this is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool. ]]> - </help> + </help> + <citations> + <citation type="bibtex">@misc{1401.1129, + Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz}, + Title = {Fast and accurate alignment of long bisulfite-seq reads}, + Year = {2014}, + Eprint = {arXiv:1401.1129}, + }</citation> + </citations> </tool>