Mercurial > repos > trinity_ctat > star_fusion
changeset 2:f90885dda34c draft
Adding star_fusion tool.
| author | trinity_ctat |
|---|---|
| date | Fri, 15 Dec 2017 14:18:29 -0500 |
| parents | 0c6f8f4e7733 |
| children | b9aeea129597 |
| files | star_fusion.xml trinity.xml |
| diffstat | 2 files changed, 8 insertions(+), 154 deletions(-) [+] |
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--- a/star_fusion.xml Fri Dec 15 14:12:30 2017 -0500 +++ b/star_fusion.xml Fri Dec 15 14:18:29 2017 -0500 @@ -1,14 +1,16 @@ -<tool id="star-fusion" name="Star Fusion" version="1.0.0" profile="17.05"> +<tool id="star_fusion" name="Star Fusion" version="1.0.0" profile="17.05"> <description>Fusion-finding Pipeline Using the STAR Aligner</description> <requirements> <requirement type="package" version="1.1.0">star-fusion</requirement> </requirements> <command detect_errors="default"> - STAR-Fusion - --genome_lib_dir "${genome_ref_lib.fields.path}" - --left_fq "${left_input} - --right_fq "${right_input} - --output_dir subdir + <![CDATA[ + STAR-Fusion + --genome_lib_dir "${genome_ref_lib.fields.path}" + --left_fq "${left_input} + --right_fq "${right_input} + --output_dir subdir + ]]> </command> <stdio> <exit_code range="1:" level="fatal" description="Error returned from pipeline" />
--- a/trinity.xml Fri Dec 15 14:12:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,148 +0,0 @@ -<tool id="trinityrnaseq" name="trinity" version="1.0.0" profile="17.05"> - - <!-- Original tool written by Jeremy Goecks, - later development/maintenance by (in chronological order) - Brian Haas, Ben Fulton, Cicada Dennis - --> - <description>De novo assembly of RNA-Seq data using Trinity 2.4.0</description> - <requirements> - <requirement type="package" version="2.7">python</requirement> - <requirement type="package">subprocess32</requirement> - <requirement type="package">samtools</requirement> - <requirement type="package">bzip2</requirement> - <requirement type="package" version="2.4.0">trinity</requirement> - </requirements> - <command detect_errors="default"> - <![CDATA[ - python $__tool_directory__/trinity_wrapper.py - --CPU \${GALAXY_SLOTS:-4} - --max_memory \${TRINITY_MAX_MEMORY:-31G} - #if str($inputs.paired_or_single) == "paired": - --left $inputs.left_input --right $inputs.right_input - #if $inputs.left_input.ext == 'fasta': - --seqType fa - #else: - --seqType fq - #end if - #else: - --single $inputs.input - #if $inputs.input.ext == 'fasta': - --seqType fa - #else: - --seqType fq - #end if - #end if - ## direct to output - --timing trinity_out_dir/Trinity.timing - --log $trinity_log - - ]]> - <!-- The fullpath, dir, and user options (preceed with dashes) can be - used in the trinity_wrapper.py command to create rerunable jobs. - We are not supporting rerunable jobs in this release of this tool. - fullpath \${TRINITY_RERUN_PREFIX} - dir '$adv.rerundir' - user $__user_id__ - mem_per_cpu 31 - --> - </command> - <stdio> - <exit_code range="1:" level="fatal" description="Program failed" /> - <exit_code range=":-1" level="fatal" description="DRM killed job" /> - </stdio> - <inputs> - <conditional name="inputs"> - <param name="paired_or_single" type="select" label="Paired or Single-end data?"> - <option value="paired">Paired</option> - <option value="single">Single</option> - </param> - <when value="paired"> - <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> - <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> - </when> - <when value="single"> - <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> - </when> - </conditional> - <!-- The following section was used to aid in creating rerunable jobs. - We are not supporting rerunable jobs in this release of this tool. - <section name="adv" title="Allow Job Rerun" expanded="False"> - <param name="rerundir" type="text" size="10" label="To make a job rerunnable, you will need to specify a unique tag to label the job, with no spaces or wierd characters." /> - </section> - --> - </inputs> - <outputs> - <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> - <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> - </outputs> - <tests> - <!-- Not testing with the following inputs anymore. - <param name="left_input" value="FLI1.left.fq" /> - <param name="right_input" value="FLI1.right.fq" /> - --> - <test> - <param name="paired_or_single" value="paired" /> - <param name="left_input" value="reads.left.simPE.fq" /> - <param name="right_input" value="reads.right.simPE.fq" /> - <param name="adv.rerundir" value="planemo_test_1" /> - <output name="trinity_log" > - <assert_contents> - <has_line_matching expression=".+" /> - <has_line line="Trinity exited with status 0" /> - </assert_contents> - </output> - <output name="assembled_transcripts" > - <assert_contents> - <has_line_matching expression=".+" /> - <has_line_matching expression=">TRINITY.+?len=.+?path=.+" /> - </assert_contents> - </output> - </test> - <test> - <param name="paired_or_single" value="paired" /> - <param name="left_input" value="Sp.cat_ds_hs.left.fq" /> - <param name="right_input" value="Sp.cat_ds_hs.right.fq" /> - <param name="adv.rerundir" value="planemo_test_2" /> - <!-- Following parameters are not used in this version of this tool. --> - <!-- - <param name="JM" value="50G" /> - <param name="CPU" value="2" /> - <param name="library_type" value="None" /> - <param name="group_pairs_distance" value="500" /> - <param name="path_reinforcement_distance" value="75" /> - <param name="use_additional" value="no" /> - --> - <output name="trinity_log" > - <assert_contents> - <has_line_matching expression=".+" /> - <has_line line="Trinity exited with status 0" /> - </assert_contents> - </output> - <output name="assembled_transcripts" > - <assert_contents> - <has_line_matching expression=".+" /> - <has_line_matching expression=">TRINITY.+?len=.+?path=.+" /> - </assert_contents> - </output> - </test> - </tests> - <help> -This instance is running Trinity version 2.4.0 and uses the following command: - - Trinity --max_memory 31G --CPU 4 --seqType seq_type --single singlefile or --left left_file --right right_file - -Define TRINITY_MAX_MEMORY and GALAXY_SLOTS to change the default values for --max_memory and --CPU, respectively. - -.. class:: infomark - -Trinity_, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. For more information, visit Trinity's wiki page here_. - -.. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki -.. _here: https://github.com/trinityrnaseq/trinityrnaseq/wiki - </help> - - <citations> - <citation type="doi">10.1038/nbt.1883</citation> - </citations> - -</tool>