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comparison align_and_estimate_abundance.xml @ 20:75f4e1859ed7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author iuc
date Tue, 11 Apr 2023 19:56:08 +0000
parents 00719b8004c9
children b2bbe9a7f1b8
comparison
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19:c2b82a94493e 20:75f4e1859ed7
1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@+galaxy1"> 1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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="bio_tools"/> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="1.3.2">rsem</requirement> 8 <requirement type="package" version="1.3.3">rsem</requirement>
9 <requirement type="package" version="0.46.0">kallisto</requirement>
10 </expand> 9 </expand>
11 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
12 ln -f -s '$transcripts' input.fa && 11 ln -f -s '$transcripts' input.fa &&
13 12
14 #if $additional_params.gene_map.has_gene_map == "yes": 13 #if $additional_params.gene_map.has_gene_map == "yes":
57 --left paired_left.fq --right paired_right.fq --seqType fq 56 --left paired_left.fq --right paired_right.fq --seqType fq
58 #else: 57 #else:
59 --left paired_left.fq.gz --right paired_right.fq.gz --seqType fq 58 --left paired_left.fq.gz --right paired_right.fq.gz --seqType fq
60 #end if 59 #end if
61 60
62 #if $inputs.strand.is_strand_specific: 61 #if $inputs.strand.is_strand_specific == 'true':
63 --SS_lib_type $inputs.strand.library_type 62 --SS_lib_type $inputs.strand.library_type
64 #end if 63 #end if
65 64
66 --max_ins_size $inputs.paired_fragment_length 65 --max_ins_size $inputs.max_ins_size
67 66
68 #else: 67 #else:
69 #if $inputs.input.is_of_type('fasta'): 68 #if $inputs.input.is_of_type('fasta'):
70 --single single.fa --seqType fa 69 --single single.fa --seqType fa
71 #else if $inputs.input.is_of_type('fastqsanger'): 70 #else if $inputs.input.is_of_type('fastqsanger'):
72 --single single.fq --seqType fq 71 --single single.fq --seqType fq
73 #else: 72 #else:
74 --single single.fq.gz --seqType fq 73 --single single.fq.gz --seqType fq
75 #end if 74 #end if
76 75
77 #if $inputs.strand.is_strand_specific: 76 #if $inputs.strand.is_strand_specific == 'true':
78 --SS_lib_type $inputs.strand.library_type 77 --SS_lib_type $inputs.strand.library_type
79 #end if 78 #end if
80 #end if 79 #end if
81 80
82 ## Additional parameters. 81 ## Additional parameters.
83 --gene_trans_map gene_to_trans.map 82 --gene_trans_map gene_to_trans.map
84
85 --prep_reference 83 --prep_reference
86
87 --output_dir output 84 --output_dir output
88 85
89 ## CPU 86 ## CPU
90 --thread_count \${GALAXY_SLOTS:-4} 87 --thread_count \${GALAXY_SLOTS:-4}
91 ]]></command> 88 ]]></command>
92 <inputs> 89 <inputs>
93 <param format="fasta" name="transcripts" argument="--transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/> 90 <param format="fasta" argument="--transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/>
94 <conditional name="inputs"> 91 <conditional name="inputs">
95 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> 92 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
96 <option value="paired">Paired</option> 93 <option value="paired">Paired</option>
97 <option value="single">Single</option> 94 <option value="single">Single</option>
98 </param> 95 </param>
99 <when value="paired"> 96 <when value="paired">
100 <param format="fasta,fastqsanger,fastqsanger.gz" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/> 97 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Left/Forward strand reads" />
101 <param format="fasta,fastqsanger,fastqsanger.gz" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/> 98 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Right/Reverse strand reads" />
102 <conditional name="strand"> 99 <conditional name="strand">
103 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 100 <param name="is_strand_specific" type="select" label="Strand specific data">
104 <when value="false"> 101 <option value="false">No</option>
105 </when> 102 <option value="true">Yes</option>
103 </param>
104 <when value="false"/>
106 <when value="true"> 105 <when value="true">
107 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> 106 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
108 <option value="FR">Forward-Reverse</option> 107 <option value="FR">Forward-Reverse</option>
109 <option value="RF">Reverse-Forward</option> 108 <option value="RF">Reverse-Forward</option>
110 </param> 109 </param>
111 </when> 110 </when>
112 </conditional> 111 </conditional>
113 <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 argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="Bowtie -X parameter"/>
114 </when> 113 </when>
115 <when value="single"> 114 <when value="single">
116 <param format="fasta,fastqsanger,fastqsanger.gz" 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=""/>
117 <conditional name="strand"> 116 <conditional name="strand">
118 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 117 <param name="is_strand_specific" type="select" label="Strand specific data">
119 <when value="false"> 118 <option value="false">No</option>
120 </when> 119 <option value="true">Yes</option>
120 </param>
121 <when value="false"/>
121 <when value="true"> 122 <when value="true">
122 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> 123 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
123 <option value="F">F</option> 124 <option value="F">F</option>
124 <option value="R">R</option> 125 <option value="R">R</option>
125 </param> 126 </param>
127 </conditional> 128 </conditional>
128 </when> 129 </when>
129 </conditional> 130 </conditional>
130 131
131 <conditional name="method"> 132 <conditional name="method">
132 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> 133 <param type="select" argument="--est_method" label="Abundance estimation method">
133 <option value="RSEM">RSEM</option> 134 <option value="RSEM">RSEM</option>
134 <option value="salmon">Salmon</option> 135 <option value="salmon">Salmon</option>
135 <option value="kallisto">Kallisto</option> 136 <option value="kallisto">Kallisto</option>
136 </param> 137 </param>
137 <when value="RSEM"> 138 <when value="RSEM">
138 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> 139 <param type="select" argument="--aln_method" label="Alignment method">
139 <option value="bowtie">Bowtie</option> 140 <option value="bowtie">Bowtie</option>
140 <option value="bowtie2">Bowtie2</option> 141 <option value="bowtie2">Bowtie2</option>
141 </param> 142 </param>
142 </when> 143 </when>
143 <when value="salmon"> 144 <when value="salmon"/>
144 </when> 145 <when value="kallisto"/>
145 <when value="kallisto">
146 </when>
147 </conditional> 146 </conditional>
148 147
149 <section name="additional_params" title="Additional Options" expanded="False"> 148 <section name="additional_params" title="Additional Options" expanded="False">
150 <conditional name="gene_map"> 149 <conditional name="gene_map">
151 <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed"> 150 <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed">
152 <option value="yes">Yes</option> 151 <option value="yes">Yes</option>
153 <option value="no">No</option> 152 <option value="no">No</option>
154 </param> 153 </param>
155 <when value="yes"> 154 <when value="yes" />
156 </when>
157 <when value="no"> 155 <when value="no">
158 <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" /> 156 <param argument="--gene_trans_map" type="data" format="tabular" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
159 </when> 157 </when>
160 </conditional> 158 </conditional>
161
162 </section> 159 </section>
163 </inputs> 160 </inputs>
164 <outputs> 161 <outputs>
165 <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/RSEM.isoforms.results"> 162 <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts (RSEM)" from_work_dir="output/RSEM.isoforms.results">
166 <filter>method['est_method'] == "RSEM"</filter> 163 <filter>method['est_method'] == "RSEM"</filter>
167 </data> 164 </data>
168 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/RSEM.genes.results"> 165 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts (RSEM)" from_work_dir="output/RSEM.genes.results">
169 <filter>method['est_method'] == "RSEM"</filter> 166 <filter>method['est_method'] == "RSEM"</filter>
170 </data> 167 </data>
171 168 <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts (Salmon)" from_work_dir="output/quant.sf">
172
173 <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf">
174 <filter>method['est_method'] == "salmon"</filter> 169 <filter>method['est_method'] == "salmon"</filter>
175 </data> 170 </data>
176 <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes"> 171 <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts (Salmon)" from_work_dir="output/quant.sf.genes">
177 <filter>method['est_method'] == "salmon"</filter> 172 <filter>method['est_method'] == "salmon"</filter>
178 </data> 173 </data>
179 174
180 <data format="tabular" name="isoforms_counts_kallisto" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/abundance.tsv"> 175 <data format="tabular" name="isoforms_counts_kallisto" label="${tool.name} on ${on_string}: isoforms counts (Kallisto)" from_work_dir="output/abundance.tsv">
181 <filter>method['est_method'] == "kallisto"</filter> 176 <filter>method['est_method'] == "kallisto"</filter>
182 </data> 177 </data>
183 <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/abundance.tsv.genes"> 178 <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts (Kallisto)" from_work_dir="output/abundance.tsv.genes">
184 <filter>method['est_method'] == "kallisto"</filter> 179 <filter>method['est_method'] == "kallisto"</filter>
185 </data> 180 </data>
186 </outputs> 181 </outputs>
187 <tests> 182 <tests>
188 <test> 183 <test>