ctat_trinity_rnaseq: ctat_trinity

annotate ctat_trinity_rnaseq.xml @ 3:777b35c8ee3e draft default tip

Trying newer trinity

author	trinity_ctat
date	Mon, 25 Jun 2018 16:38:28 -0400
parents	8291ea96690f
children

rev	line source
0 6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	1 <tool id="ctat_trinity_rnaseq" name="ctat_trinity_rnaseq" version="1.0.0" profile="17.05">
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	2
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	3 <!-- Original tool written by Jeremy Goecks,
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	4 later development/maintenance by (in chronological order)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	5 Brian Haas, Ben Fulton, Cicada Dennis
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	6 -->
3 777b35c8ee3e Trying newer trinity trinity_ctat parents: 2 diff changeset	7 <description>De novo assembly of RNA-Seq data using Trinity</description>
0 6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	8 <requirements>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	9 <requirement type="package" version="2.7">python</requirement>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	10 <requirement type="package">subprocess32</requirement>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	11 <requirement type="package">bzip2</requirement>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	12 <requirement type="package" version="1.3.0">rsem</requirement>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	13 <requirement type="package" version="3">bioconductor-edger</requirement>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	14 <requirement type="package" version="2">bioconductor-qvalue</requirement>
3 777b35c8ee3e Trying newer trinity trinity_ctat parents: 2 diff changeset	15 <requirement type="package" version="2.6.6">trinity</requirement>
0 6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	16 </requirements>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	17 <command detect_errors="default">
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	18 <![CDATA[
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	19 python $__tool_directory__/ctat_trinity_wrapper.py
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	20 --CPU \${GALAXY_SLOTS:-4}
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	21 --max_memory \${TRINITY_MAX_MEMORY:-31G}
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	22 #if str($inputs.paired_or_single) == "paired":
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	23 --left $inputs.left_input --right $inputs.right_input
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	24 #if $inputs.left_input.ext == 'fasta':
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	25 --seqType fa
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	26 #else:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	27 --seqType fq
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	28 #end if
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	29 #else:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	30 --single $inputs.input
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	31 #if $inputs.input.ext == 'fasta':
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	32 --seqType fa
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	33 #else:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	34 --seqType fq
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	35 #end if
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	36 #end if
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	37 ## direct to output
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	38 --timing trinity_out_dir/Trinity.timing
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	39 --log $trinity_log
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	40
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	41 ]]>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	42 <!-- The fullpath, dir, and user options (preceed with dashes) can be
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	43 used in the ctat_trinity_wrapper.py command to create rerunable jobs.
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	44 We are not supporting rerunable jobs in this release of this tool.
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	45 fullpath \${TRINITY_RERUN_PREFIX}
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	46 dir '$adv.rerundir'
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	47 user $__user_id__
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	48 mem_per_cpu 31
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	49 -->
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	50 </command>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	51 <stdio>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	52 <exit_code range="1:" level="fatal" description="Program failed" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	53 <exit_code range=":-1" level="fatal" description="DRM killed job" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	54 </stdio>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	55 <inputs>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	56 <conditional name="inputs">
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	57 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	58 <option value="paired">Paired</option>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	59 <option value="single">Single</option>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	60 </param>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	61 <when value="paired">
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	62 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	63 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	64 </when>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	65 <when value="single">
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	66 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	67 </when>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	68 </conditional>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	69 <!-- The following section was used to aid in creating rerunable jobs.
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	70 We are not supporting rerunable jobs in this release of this tool.
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	71 <section name="adv" title="Allow Job Rerun" expanded="False">
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	72 <param name="rerundir" type="txt" 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." />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	73 </section>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	74 -->
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	75 </inputs>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	76 <outputs>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	77 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	78 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	79 </outputs>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	80 <tests>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	81 <!-- Not testing with the following inputs anymore.
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	82 <param name="left_input" value="FLI1.left.fq" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	83 <param name="right_input" value="FLI1.right.fq" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	84 -->
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	85 <test>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	86 <param name="paired_or_single" value="paired" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	87 <param name="left_input" value="reads.left.simPE.fq" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	88 <param name="right_input" value="reads.right.simPE.fq" />
2 8291ea96690f Fixing error in ctat_abundance_estimation_to_matrix.xml. trinity_ctat parents: 0 diff changeset	89 <!-- Not using in public version of tool
0 6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	90 <param name="adv.rerundir" value="planemo_test_1" />
2 8291ea96690f Fixing error in ctat_abundance_estimation_to_matrix.xml. trinity_ctat parents: 0 diff changeset	91 -->
0 6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	92 <output name="trinity_log" >
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	93 <assert_contents>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	94 <has_line_matching expression=".+" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	95 <has_line line="Trinity exited with status 0" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	96 </assert_contents>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	97 </output>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	98 <output name="assembled_transcripts" >
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	99 <assert_contents>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	100 <has_line_matching expression=".+" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	101 <has_line_matching expression=">TRINITY.+?len=.+?path=.+" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	102 </assert_contents>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	103 </output>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	104 </test>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	105 <test>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	106 <param name="paired_or_single" value="paired" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	107 <param name="left_input" value="Sp.cat_ds_hs.left.fq" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	108 <param name="right_input" value="Sp.cat_ds_hs.right.fq" />
2 8291ea96690f Fixing error in ctat_abundance_estimation_to_matrix.xml. trinity_ctat parents: 0 diff changeset	109 <!-- Not using in public version of tool
0 6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	110 <param name="adv.rerundir" value="planemo_test_2" />
2 8291ea96690f Fixing error in ctat_abundance_estimation_to_matrix.xml. trinity_ctat parents: 0 diff changeset	111 -->
0 6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	112 <!-- Following parameters are not used in this version of this tool. -->
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	113 <!--
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	114 <param name="JM" value="50G" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	115 <param name="CPU" value="2" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	116 <param name="library_type" value="None" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	117 <param name="group_pairs_distance" value="500" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	118 <param name="path_reinforcement_distance" value="75" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	119 <param name="use_additional" value="no" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	120 -->
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	121 <output name="trinity_log" >
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	122 <assert_contents>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	123 <has_line_matching expression=".+" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	124 <has_line line="Trinity exited with status 0" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	125 </assert_contents>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	126 </output>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	127 <output name="assembled_transcripts" >
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	128 <assert_contents>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	129 <has_line_matching expression=".+" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	130 <has_line_matching expression=">TRINITY.+?len=.+?path=.+" />
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	131 </assert_contents>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	132 </output>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	133 </test>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	134 </tests>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	135 <help>
3 777b35c8ee3e Trying newer trinity trinity_ctat parents: 2 diff changeset	136 This instance runs Trinity with the following command:
0 6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	137
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	138 Trinity --max_memory 31G --CPU 4 --seqType seq_type --single singlefile or --left left_file --right right_file
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	139
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	140 Define TRINITY_MAX_MEMORY and GALAXY_SLOTS to change the default values for --max_memory and --CPU, respectively.
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	141
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	142 .. class:: infomark
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	143
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	144 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_.
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	145
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	146 .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	147 .. _here: https://github.com/trinityrnaseq/trinityrnaseq/wiki
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	148 </help>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	149
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	150 <citations>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	151 <citation type="doi">10.1038/nbt.1883</citation>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	152 </citations>
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	153
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	154 </tool>

Mercurial > repos > trinity_ctat > ctat_trinity_rnaseq

annotate ctat_trinity_rnaseq.xml @ 3:777b35c8ee3e draft default tip