Mercurial > repos > iuc > trinity_align_and_estimate_abundance

comparison align_and_estimate_abundance.xml @ 16:893655fa55f9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
author iuc
date Fri, 19 Mar 2021 21:48:30 +0000
parents 56162e446004
children 6c20d62180af
comparison
equal deleted inserted replaced
15:56162e446004 16:893655fa55f9
1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@"> 1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@+galaxy1">
2 <description>on a de novo assembly of RNA-Seq data</description> 2 <description>on a 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 18
19 #if $inputs.paired_or_single == "paired": 19 #if $inputs.paired_or_single == "paired":
20 #if $inputs.left_input.is_of_type('fasta'): 20 #if $inputs.left_input.is_of_type('fasta'):
21 ln -s '$inputs.left_input' paired_left.fa && 21 ln -s '$inputs.left_input' paired_left.fa &&
22 ln -s '$inputs.right_input' paired_right.fa 22 ln -s '$inputs.right_input' paired_right.fa
23 #else: 23 #else if $inputs.left_input.is_of_type('fastqsanger'):
24 ln -s '$inputs.left_input' paired_left.fq && 24 ln -s '$inputs.left_input' paired_left.fq &&
25 ln -s '$inputs.right_input' paired_right.fq 25 ln -s '$inputs.right_input' paired_right.fq
26 #else:
27 ln -s '$inputs.left_input' paired_left.fq.gz &&
28 ln -s '$inputs.right_input' paired_right.fq.gz
26 #end if 29 #end if
27 #else: 30 #else:
28 #if $inputs.input.is_of_type('fasta'): 31 #if $inputs.input.is_of_type('fasta'):
29 ln -s '$inputs.input' single.fa 32 ln -s '$inputs.input' single.fa
33 #else if $inputs.input.is_of_type('fastqsanger'):
34 ln -s '$inputs.input' single.fq
30 #else: 35 #else:
31 ln -s '$inputs.input' single.fq 36 ln -s '$inputs.input' single.fq.gz
32 #end if 37 #end if
33 #end if 38 #end if
34 39
35 && 40 &&
36 41
45 50
46 #if $inputs.paired_or_single == "paired": 51 #if $inputs.paired_or_single == "paired":
47 52
48 #if $inputs.left_input.is_of_type('fasta'): 53 #if $inputs.left_input.is_of_type('fasta'):
49 --left paired_left.fa --right paired_right.fa --seqType fa 54 --left paired_left.fa --right paired_right.fa --seqType fa
55 #else if $inputs.left_input.is_of_type('fastqsanger'):
56 --left paired_left.fq --right paired_right.fq --seqType fq
50 #else: 57 #else:
51 --left paired_left.fq --right paired_right.fq --seqType fq 58 --left paired_left.fq.gz --right paired_right.fq.gz --seqType fq
52 #end if 59 #end if
53 60
54 #if $inputs.strand.is_strand_specific: 61 #if $inputs.strand.is_strand_specific:
55 --SS_lib_type $inputs.strand.library_type 62 --SS_lib_type $inputs.strand.library_type
56 #end if 63 #end if
58 --max_ins_size $inputs.paired_fragment_length 65 --max_ins_size $inputs.paired_fragment_length
59 66
60 #else: 67 #else:
61 #if $inputs.input.is_of_type('fasta'): 68 #if $inputs.input.is_of_type('fasta'):
62 --single single.fa --seqType fa 69 --single single.fa --seqType fa
70 #else if $inputs.input.is_of_type('fastqsanger'):
71 --single single.fq --seqType fq
63 #else: 72 #else:
64 --single single.fq --seqType fq 73 --single single.fq.gz --seqType fq
65 #end if 74 #end if
66 75
67 #if $inputs.strand.is_strand_specific: 76 #if $inputs.strand.is_strand_specific:
68 --SS_lib_type $inputs.strand.library_type 77 --SS_lib_type $inputs.strand.library_type
69 #end if 78 #end if
85 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> 94 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
86 <option value="paired">Paired</option> 95 <option value="paired">Paired</option>
87 <option value="single">Single</option> 96 <option value="single">Single</option>
88 </param> 97 </param>
89 <when value="paired"> 98 <when value="paired">
90 <param format="fasta,fastqsanger" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/> 99 <param format="fasta,fastqsanger,fastqsanger.gz" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/>
91 <param format="fasta,fastqsanger" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/> 100 <param format="fasta,fastqsanger,fastqsanger.gz" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/>
92 <conditional name="strand"> 101 <conditional name="strand">
93 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 102 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
94 <when value="false"> 103 <when value="false">
95 </when> 104 </when>
96 <when value="true"> 105 <when value="true">
101 </when> 110 </when>
102 </conditional> 111 </conditional>
103 <param name="paired_fragment_length" argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/> 112 <param name="paired_fragment_length" argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/>
104 </when> 113 </when>
105 <when value="single"> 114 <when value="single">
106 <param format="fasta,fastqsanger" argument="--single" name="input" type="data" label="Single-end reads" help=""/> 115 <param format="fasta,fastqsanger,fastqsanger.gz" argument="--single" name="input" type="data" label="Single-end reads" help=""/>
107 <conditional name="strand"> 116 <conditional name="strand">
108 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 117 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
109 <when value="false"> 118 <when value="false">
110 </when> 119 </when>
111 <when value="true"> 120 <when value="true">
175 </data> 184 </data>
176 </outputs> 185 </outputs>
177 <tests> 186 <tests>
178 <test> 187 <test>
179 <param name="paired_or_single" value="paired"/> 188 <param name="paired_or_single" value="paired"/>
180 <param name="left_input" value="reads.left.fq"/> 189 <param name="left_input" value="reads.left.fq.gz"/>
181 <param name="right_input" value="reads.right.fq"/> 190 <param name="right_input" value="reads.right.fq.gz"/>
182 <param name="transcripts" value="raw/Trinity.fasta"/> 191 <param name="transcripts" value="raw/Trinity.fasta"/>
183 <param name="gene_to_trans" value="raw/Trinity.map" /> 192 <param name="gene_to_trans" value="raw/Trinity.map" />
184 <param name="library_type" value="RF"/> 193 <param name="library_type" value="RF"/>
185 <param name="est_method" value="RSEM"/> 194 <param name="est_method" value="RSEM"/>
186 <param name="aln_method" value="bowtie"/> 195 <param name="aln_method" value="bowtie"/>