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comparison trinity.xml @ 18:d3b1249af60c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
author iuc
date Tue, 19 Dec 2017 04:21:46 -0500
parents 199aa6821ca5
children cee61b3fcf78
comparison
equal deleted inserted replaced
17:199aa6821ca5 18:d3b1249af60c
1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.1"> 1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.2">
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" />
7 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 Trinity --no_version_check 8 #if $additional_params.guided.is_guided == "yes":
9 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
10 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
11 #end if
12 Trinity --no_version_check
9 13
10 ## Inputs. 14 ## Inputs.
11 #if $inputs.paired_or_single == "paired": 15 #if $inputs.paired_or_single == "paired":
12 16
13 --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) } 17 --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) }
57 #end if 61 #end if
58 #if $additional_params.long_reads: 62 #if $additional_params.long_reads:
59 --long_reads $additional_params.long_reads 63 --long_reads $additional_params.long_reads
60 #end if 64 #end if
61 #if $additional_params.guided.is_guided == "yes": 65 #if $additional_params.guided.is_guided == "yes":
62 --genome_guided_bam $additional_params.guided.genome_guided_bam 66 --genome_guided_bam 'localbam.bam'
63 67
64 #if $additional_params.guided.genome_guided_min_coverage: 68 #if $additional_params.guided.genome_guided_min_coverage:
65 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage 69 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
66 #end if 70 #end if
67 71
68 #if $additional_params.guided.genome_guided_min_reads_per_partition: 72 #if $additional_params.guided.genome_guided_min_reads_per_partition:
69 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition 73 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
74 #end if
75
76 #if $additional_params.guided.genome_guided_max_intron:
77 --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron
70 #end if 78 #end if
71 79
72 #end if 80 #end if
73 81
74 #if $additional_params.min_kmer_cov: 82 #if $additional_params.min_kmer_cov:
123 <option value="yes">Yes</option> 131 <option value="yes">Yes</option>
124 </param> 132 </param>
125 <when value="no"> 133 <when value="no">
126 </when> 134 </when>
127 <when value="yes"> 135 <when value="yes">
128 <param name="genome_guided_bam" argument="--genome_guided_bam" type="data" format="bam" label="Coordinate-sorted BAM file" /> 136 <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
137 <param name="genome_guided_max_intron" argument="--genome_guided_max_intron" type="integer" value="" min="1" label="Maximum allowed intron length (also maximum fragment span on 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"/> 138 <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"/>
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"/> 139 <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"/>
131 </when> 140 </when>
132 </conditional> 141 </conditional>
133 142