trinity: trinity.xml annotate

annotate trinity.xml @ 3:962f40c5958c draft default tip

Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.

author	trinity_ctat
date	Fri, 06 Oct 2017 10:56:47 -0400
parents	7824ba3f1dfc
children

rev	line source
3 962f40c5958c Adding profile info and exit code behavior. Making version numbers consistent. Upping test number. trinity_ctat parents: 2 diff changeset	1 <tool id="trinityrnaseq" name="trinity" version="1.0.0" profile="17.05">
0 f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	2
1 88ada07f855c Adding align_and_estimate_abundance tool. trinity_ctat parents: 0 diff changeset	3 <!-- Original tool written by Jeremy Goecks,
0 f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	4 later development/maintenance by (in chronological order)
1 88ada07f855c Adding align_and_estimate_abundance tool. trinity_ctat parents: 0 diff changeset	5 Brian Haas, Ben Fulton, Cicada Dennis
0 f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	6 -->
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	7 <description>De novo assembly of RNA-Seq data using Trinity 2.4.0</description>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	8 <requirements>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	9 <requirement type="package" version="2.7">python</requirement>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	10 <requirement type="package">subprocess32</requirement>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	11 <requirement type="package">samtools</requirement>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	12 <requirement type="package">bzip2</requirement>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	13 <requirement type="package" version="2.4.0">trinity</requirement>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	14 </requirements>
3 962f40c5958c Adding profile info and exit code behavior. Making version numbers consistent. Upping test number. trinity_ctat parents: 2 diff changeset	15 <command detect_errors="default">
0 f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	16 <![CDATA[
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	17 python $__tool_directory__/trinity_wrapper.py
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	18 --CPU \${GALAXY_SLOTS:-4}
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	19 --max_memory \${TRINITY_MAX_MEMORY:-31G}
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	20 #if str($inputs.paired_or_single) == "paired":
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	21 --left $inputs.left_input --right $inputs.right_input
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	22 #if $inputs.left_input.ext == 'fasta':
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	23 --seqType fa
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	24 #else:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	25 --seqType fq
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	26 #end if
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	27 #else:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	28 --single $inputs.input
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	29 #if $inputs.input.ext == 'fasta':
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	30 --seqType fa
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	31 #else:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	32 --seqType fq
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	33 #end if
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	34 #end if
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	35 ## direct to output
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	36 --timing trinity_out_dir/Trinity.timing
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	37 --log $trinity_log
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	38
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	39 ]]>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	40 <!-- The fullpath, dir, and user options (preceed with dashes) can be
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	41 used in the trinity_wrapper.py command to create rerunable jobs.
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	42 We are not supporting rerunable jobs in this release of this tool.
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	43 fullpath \${TRINITY_RERUN_PREFIX}
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	44 dir '$adv.rerundir'
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	45 user $__user_id__
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	46 mem_per_cpu 31
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	47 -->
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	48 </command>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	49 <stdio>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	50 <exit_code range="1:" level="fatal" description="Program failed" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	51 <exit_code range=":-1" level="fatal" description="DRM killed job" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	52 </stdio>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	53 <inputs>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	54 <conditional name="inputs">
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	55 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	56 <option value="paired">Paired</option>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	57 <option value="single">Single</option>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	58 </param>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	59 <when value="paired">
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	60 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	61 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	62 </when>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	63 <when value="single">
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	64 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	65 </when>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	66 </conditional>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	67 <!-- The following section was used to aid in creating rerunable jobs.
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	68 We are not supporting rerunable jobs in this release of this tool.
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	69 <section name="adv" title="Allow Job Rerun" expanded="False">
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	70 <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." />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	71 </section>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	72 -->
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	73 </inputs>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	74 <outputs>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	75 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	76 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	77 </outputs>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	78 <tests>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	79 <!-- Not testing with the following inputs anymore.
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	80 <param name="left_input" value="FLI1.left.fq" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	81 <param name="right_input" value="FLI1.right.fq" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	82 -->
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	83 <test>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	84 <param name="paired_or_single" value="paired" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	85 <param name="left_input" value="reads.left.simPE.fq" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	86 <param name="right_input" value="reads.right.simPE.fq" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	87 <param name="adv.rerundir" value="planemo_test_1" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	88 <output name="trinity_log" >
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	89 <assert_contents>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	90 <has_line_matching expression=".+" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	91 <has_line line="Trinity exited with status 0" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	92 </assert_contents>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	93 </output>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	94 <output name="assembled_transcripts" >
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	95 <assert_contents>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	96 <has_line_matching expression=".+" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	97 <has_line_matching expression=">TRINITY.+?len=.+?path=.+" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	98 </assert_contents>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	99 </output>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	100 </test>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	101 <test>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	102 <param name="paired_or_single" value="paired" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	103 <param name="left_input" value="Sp.cat_ds_hs.left.fq" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	104 <param name="right_input" value="Sp.cat_ds_hs.right.fq" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	105 <param name="adv.rerundir" value="planemo_test_2" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	106 <!-- Following parameters are not used in this version of this tool. -->
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	107 <!--
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	108 <param name="JM" value="50G" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	109 <param name="CPU" value="2" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	110 <param name="library_type" value="None" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	111 <param name="group_pairs_distance" value="500" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	112 <param name="path_reinforcement_distance" value="75" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	113 <param name="use_additional" value="no" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	114 -->
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	115 <output name="trinity_log" >
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	116 <assert_contents>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	117 <has_line_matching expression=".+" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	118 <has_line line="Trinity exited with status 0" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	119 </assert_contents>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	120 </output>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	121 <output name="assembled_transcripts" >
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	122 <assert_contents>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	123 <has_line_matching expression=".+" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	124 <has_line_matching expression=">TRINITY.+?len=.+?path=.+" />
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	125 </assert_contents>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	126 </output>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	127 </test>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	128 </tests>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	129 <help>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	130 This instance is running Trinity version 2.4.0 and uses the following command:
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	131
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	132 Trinity --max_memory 31G --CPU 4 --seqType seq_type --single singlefile or --left left_file --right right_file
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	133
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	134 Define TRINITY_MAX_MEMORY and GALAXY_SLOTS to change the default values for --max_memory and --CPU, respectively.
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	135
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	136 .. class:: infomark
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	137
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	138 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_.
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	139
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	140 .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	141 .. _here: https://github.com/trinityrnaseq/trinityrnaseq/wiki
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	142 </help>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	143
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	144 <citations>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	145 <citation type="doi">10.1038/nbt.1883</citation>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	146 </citations>
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	147
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	148 </tool>

Mercurial > repos > trinity_ctat > trinity

annotate trinity.xml @ 3:962f40c5958c draft default tip