Mercurial > repos > jjohnson > trinityrnaseq

annotate trinityrnaseq_norm.xml @ 8:233f2f5169f8

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Change hmmer tool_dependency to iuc
author Jim Johnson <jj@umn.edu>
date Thu, 06 Feb 2014 09:33:47 -0600
parents 5eb99d21ef0d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
1 <tool id="trinityrnaseq_norm" name="Trinity read normalization" version="0.0.2">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
2 <!-- Written by Jeremy Goecks, modified by Josh Bowden for normalization proceedure, now maintained here by bhaas -->
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
3 <description>Pre-process RNA-seq data to reduce coverage of highly covered areas</description>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
4 <requirements>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
5 <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
6 </requirements>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
7 <command>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
8 ## symlink input in work_dir
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
9 #if str($inputs.paired_or_single) == "paired":
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
10 ln -s $inputs.left_input left_reads &amp;&amp;
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
11 ln -s $inputs.right_input right_reads &amp;&amp;
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
12 #else:
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
13 ln -s $inputs.input single_reads &amp;&amp;
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
14 #end if
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
15 \${TRINITY_HOME}/util/normalize_by_kmer_coverage.pl --JM $JM --max_cov $max_cov
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
16 ## Inputs.
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
17 #if str($inputs.paired_or_single) == "paired":
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
18 --left left_reads --right right_reads
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
19 #if $inputs.left_input.ext == 'fa':
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
20 --seqType fa
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
21 #else:
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
22 --seqType fq
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
23 #end if
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
24 $inputs.pe_reads_unordered
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
25 #if str($inputs.library_type) != "None":
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
26 --SS_lib_type $inputs.library_type
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
27 #end if
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
28 $inputs.pairs_together
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
29 $inputs.parallel_stats
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
30 #else:
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
31 --single single_reads
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
32 #if str($inputs.input.ext) == 'fa':
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
33 --seqType fa
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
34 #else:
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
35 --seqType fq
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
36 #end if
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
37 #if str($inputs.library_type) != "None":
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
38 --SS_lib_type $inputs.library_type
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
39 #end if
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
40 #end if
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
41 #if $kmer_size:
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
42 --KMER_SIZE $kmer_size
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
43 #end if
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
44 #if $max_pct_stdev:
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
45 --max_pct_stdev $max_pct_stdev
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
46 #end if
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
47 ## direct stdio to output
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
48 | tee $trinity_coverage_normalization_log &amp;&amp;
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
49 #if str($inputs.paired_or_single) == "paired":
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
50 cp left_reads.normalized* $output_left &amp;&amp;
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
51 cp right_reads.normalized* $output_right
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
52 #else:
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
53 cp single_reads.normalized* $output_single
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
54 #end if
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
55 </command>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
56 <inputs>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
57 <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
58 <option value="1G">1G</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
59 <option value="10G">10G</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
60 <option value="20G">20G</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
61 <option value="50G">50G</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
62 <option value="100G">100G</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
63 </param>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
64
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
65 <param name="max_cov" type="select" label="max_cov" help="Read coverage in terms of maximum covarge to keep">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
66 <option value="30">30</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
67 <option value="40">40</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
68 <option value="50">50</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
69 <option value="60">60</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
70 <option value="70">70</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
71 <option value="100">100</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
72 </param>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
73
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
74 <conditional name="inputs">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
75 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
76 <option value="paired">Paired</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
77 <option value="single">Single</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
78 </param>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
79 <when value="paired">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
80 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
81 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
82 <param name="library_type" type="select" label="Strand-specific Library Type">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
83 <option value="None">None</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
84 <option value="FR">FR</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
85 <option value="RF">RF</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
86 </param>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
87 <param name="pe_reads_unordered" type="boolean" truevalue="--PE_reads_unordered" falsevalue="" checked="false" label="set if the input paired-end reads are not identically ordered"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
88 <param name="pairs_together" type="boolean" truevalue="--pairs_together" falsevalue="" checked="false" label="process paired reads by averaging stats between pairs and retaining linking info"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
89 <param name="parallel_stats" type="boolean" truevalue="--PARALLEL_STATS" falsevalue="" checked="false" label="generate read stats in parallel for paired reads" help="(Figure 2X Inchworm memory requirement)"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
90 </when>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
91 <when value="single">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
92 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
93 <param name="library_type" type="select" label="Strand-specific Library Type">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
94 <option value="None">None</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
95 <option value="F">F</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
96 <option value="R">R</option>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
97 </param>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
98 </when>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
99 </conditional>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
100 <param name="kmer_size" type="integer" value="" optional="true" label="KMER SIZE" help="default: 25">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
101 <validator type="in_range" message="kmer size between 3 and 200" min="3" max="200"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
102 </param>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
103 <param name="max_pct_stdev" type="integer" value="" optional="true" label="maximum pct of mean for stdev of kmer coverage across read" help="default: 100">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
104 <validator type="in_range" message="kmer size between 10 and 100" min="10" max="100"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
105 </param>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
106
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
107 </inputs>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
108 <stdio>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
109 <exit_code range="1:" level="fatal" description="Failed" />
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
110 <regex match="Error"
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
111 source="stdout"
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
112 level="fatal"
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
113 description="Failed" />
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
114 </stdio>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
115 <outputs>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
116 <!-- I have not found a way to do condional outputs so all potential output files are specified and some will be empty -->
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
117 <data format="txt" name="trinity_coverage_normalization_log" label="${tool.name} on ${on_string}: log" />
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
118 <data format_source="left_input" name="output_left" label="${tool.name} on ${on_string}: Normalized left reads">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
119 <filter>inputs['paired_or_single'] == "paired"</filter>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
120 </data>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
121 <data format_source="right_input" name="output_right" label="${tool.name} on ${on_string}: Normalized right reads">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
122 <filter>inputs['paired_or_single'] == "paired"</filter>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
123 </data>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
124 <data format_source="input" name="output_single" label="${tool.name} on ${on_string}: Normalized reads">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
125 <filter>inputs['paired_or_single'] == "single"</filter>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
126 </data>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
127 </outputs>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
128 <tests>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
129 <test>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
130 <param name="JM" value="1G"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
131 <param name="max_cov" value="30"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
132 <param name="paired_or_single" value="single"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
133 <param name="input" ftype="fastq" value="reads.left.fq"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
134 <param name="library_type" value="None"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
135 <output name="trinity_coverage_normalization_log">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
136 <assert_contents>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
137 <has_text text="Normalization complete." />
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
138 </assert_contents>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
139 </output>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
140 <output name="output_single">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
141 <assert_contents>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
142 <has_text text="ACTGCATCCTGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTTT" />
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
143 </assert_contents>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
144 </output>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
145 </test>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
146 <test>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
147 <param name="JM" value="1G"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
148 <param name="max_cov" value="30"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
149 <param name="paired_or_single" value="paired"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
150 <param name="left_input" ftype="fastq" value="reads.left.fq"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
151 <param name="right_input" ftype="fastq" value="reads.right.fq"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
152 <param name="library_type" value="None"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
153 <param name="pe_reads_unordered" value="False"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
154 <param name="pairs_together" value="False"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
155 <param name="parallel_stats" value="False"/>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
156 <output name="trinity_coverage_normalization_log">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
157 <assert_contents>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
158 <has_text text="Normalization complete." />
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
159 </assert_contents>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
160 </output>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
161 <output name="output_left">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
162 <assert_contents>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
163 <has_text text="CTGGGCTGCAGCTAAGTTCTCTGCATCCTCCTTCTTGCTTGTGGCTGGGAAGAAGACAATGTTGTCGATGGTCTGG" />
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
164 </assert_contents>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
165 </output>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
166 <output name="output_right">
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
167 <assert_contents>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
168 <has_text text="CTCAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGC" />
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
169 </assert_contents>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
170 </output>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
171 </test>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
172 </tests>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
173 <help>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
174 Runs script Trinity_ script util/normalize_by_kmer_coverage.pl which reduces data sizes with minimal impact on recovered transcripts when used by Trinity.pl.
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
175
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
176 .. _Trinity: http://trinityrnaseq.sourceforge.net
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
177 </help>
5eb99d21ef0d Add trinityrnaseq_norm and transcriptsToOrfs tools
Jim Johnson <jj@umn.edu>
parents:
diff changeset
178 </tool>