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comparison trinity.xml @ 18:87ab70ffdf1f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
author iuc
date Fri, 15 Dec 2017 07:53:25 -0500
parents 7c21b4380e84
children f07bc380d66c
comparison
equal deleted inserted replaced
17:b9b604bcd85b 18:87ab70ffdf1f
1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.0"> 1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.1">
2 <description>de novo assembly of RNA-Seq data</description> 2 <description>de novo assembly of RNA-Seq data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
18 --seqType fa 18 --seqType fa
19 #else: 19 #else:
20 --seqType fq 20 --seqType fq
21 #end if 21 #end if
22 22
23 #if $inputs.strand.is_strand_specific: 23 @COMMAND_PAIRED_STRAND_JACCARD@
24 --SS_lib_type $inputs.strand.library_type 24
25 #elif $inputs.paired_or_single == "paired_collection"
26 --left ${ ','.join(['"%s"' % x.forward for x in $inputs.pair_input]) }
27
28 --right ${ ','.join(['"%s"' % x.reverse for x in $inputs.pair_input]) }
29
30 #if $inputs.pair_input[0].forward.is_of_type('fasta'):
31 --seqType fa
32 #else:
33 --seqType fq
25 #end if 34 #end if
26 35
27 $inputs.jaccard_clip 36 @COMMAND_PAIRED_STRAND_JACCARD@
28 37
29 #else: 38 #else:
30 --single ${ ','.join(['"%s"' % x for x in $inputs.input]) } 39 --single ${ ','.join(['"%s"' % x for x in $inputs.input]) }
31 40
32 #if $inputs.input[0].is_of_type('fasta'): 41 #if $inputs.input[0].is_of_type('fasta'):
72 ## > $trinity_log 2>&1 81 ## > $trinity_log 2>&1
73 ]]></command> 82 ]]></command>
74 <inputs> 83 <inputs>
75 <conditional name="inputs"> 84 <conditional name="inputs">
76 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> 85 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
77 <option value="paired">Paired</option> 86 <option value="single">Single-end</option>
78 <option value="single">Single</option> 87 <option value="paired" selected="true">Paired-end</option>
88 <option value="paired_collection">Paired-end collection</option>
79 </param> 89 </param>
80 <when value="paired">
81 <param format="fasta,fastqsanger" argument="--left" name="left_input" multiple="true" type="data" label="Left/Forward strand reads" help=""/>
82 <param format="fasta,fastqsanger" argument="--right" name="right_input" multiple="true" type="data" label="Right/Reverse strand reads" help=""/>
83 <conditional name="strand">
84 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
85 <when value="false">
86 </when>
87 <when value="true">
88 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
89 <option value="FR">Forward-Reverse</option>
90 <option value="RF">Reverse-Forward</option>
91 </param>
92 </when>
93 </conditional>
94 <param name="jaccard_clip" argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="set if you expect high gene density with UTR overlap"/>
95 </when>
96 <when value="single"> 90 <when value="single">
97 <param format="fasta,fastqsanger" name="input" argument="--single" multiple="true" type="data" label="Single-end reads" help=""/> 91 <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/>
98 <conditional name="strand"> 92 <conditional name="strand">
99 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 93 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
100 <when value="false"> 94 <when value="false">
101 </when> 95 </when>
102 <when value="true"> 96 <when value="true">
104 <option value="F">F</option> 98 <option value="F">F</option>
105 <option value="R">R</option> 99 <option value="R">R</option>
106 </param> 100 </param>
107 </when> 101 </when>
108 </conditional> 102 </conditional>
103 </when>
104 <when value="paired">
105 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" />
106 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" />
107 <expand macro="input_paired_strand_jaccard" />
108 </when>
109 <when value="paired_collection">
110 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/>
111 <expand macro="input_paired_strand_jaccard" />
109 </when> 112 </when>
110 </conditional> 113 </conditional>
111 114
112 <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/> 115 <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
113 116
120 <option value="yes">Yes</option> 123 <option value="yes">Yes</option>
121 </param> 124 </param>
122 <when value="no"> 125 <when value="no">
123 </when> 126 </when>
124 <when value="yes"> 127 <when value="yes">
125 <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" /> 128 <param name="genome_guided_bam" argument="--genome_guided_bam" type="data" format="bam" label="Coordinate-sorted BAM file" />
126 <param name="genome_guided_min_coverage" argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/> 129 <param name="genome_guided_min_coverage" argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
127 <param name="genome_guided_min_reads_per_partition" argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/> 130 <param name="genome_guided_min_reads_per_partition" argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
128 </when> 131 </when>
129 </conditional> 132 </conditional>
130 133
131 <param format="fasta" name="long_reads" argument="--long_reads" type="data" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/> 134 <param name="long_reads" argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
132 135
133 <param name="min_kmer_cov" argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/> 136 <param name="min_kmer_cov" argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
134 </section> 137 </section>
135 </inputs> 138 </inputs>
136 <outputs> 139 <outputs>
137 <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /--> 140 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
138 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
139 </outputs> 141 </outputs>
140 <tests> 142 <tests>
141 <test> 143 <test>
142 <param name="paired_or_single" value="paired"/> 144 <param name="paired_or_single" value="paired"/>
143 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> 145 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
154 <param name="is_strand_specific" value="true"/> 156 <param name="is_strand_specific" value="true"/>
155 <param name="norm" value="true"/> 157 <param name="norm" value="true"/>
156 <param name="library_type" value="RF"/> 158 <param name="library_type" value="RF"/>
157 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> 159 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
158 </test> 160 </test>
161 <test>
162 <param name="paired_or_single" value="paired_collection"/>
163 <param name="pair_input">
164 <collection type="list:paired">
165 <element name="pair1">
166 <collection type="paired">
167 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
168 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
169 </collection>
170 </element>
171 <element name="pair2">
172 <collection type="paired">
173 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
174 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
175 </collection>
176 </element>
177 </collection>
178 </param>
179 <param name="is_strand_specific" value="true"/>
180 <param name="norm" value="true"/>
181 <param name="library_type" value="RF"/>
182 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
183 </test>
159 </tests> 184 </tests>
160 <help> 185 <help>
161 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. 186 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
162 187
163 .. _Trinity: http://trinityrnaseq.github.io 188 .. _Trinity: http://trinityrnaseq.github.io
164 </help> 189 </help>
165 190
166 <expand macro="citation" /> 191 <expand macro="citation" />
167 </tool> 192 </tool>