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comparison tximport.xml @ 0:206a71a69161 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
author iuc
date Wed, 04 Dec 2019 05:57:26 -0500
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children 2c338211927c
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-1:000000000000 0:206a71a69161
1 <tool id="tximport" name="tximport" version="0.1">
2 <description>Summarize transcript-level estimates for gene-level analysis</description>
3 <requirements>
4 <requirement type="package">bioconductor-tximport</requirement>
5 <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
6 <requirement type="package" version="1.20.2">r-getopt</requirement>
7 </requirements>
8
9 <stdio>
10 <exit_code range="1:" level="fatal" description="Error code returned" />
11 <regex match="is not TRUE"
12 source="both"
13 level="fatal"
14 description="Execution halted." />
15 </stdio>
16
17 <command><![CDATA[
18 #if $gene_id_source_selector.gene_id_source == 'external_file':
19 #if $gene_id_source_selector.gff_source_selector.gff_source == 'history':
20 #if $gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.mapping_file_option == 'gff_gtf':
21 ln -s '$gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.own_gff' mapping.gff &&
22 #else:
23 ln -s '$gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.own_tx2gene' mapping.tab &&
24 #end if
25 #end if
26 #end if
27
28 Rscript '${__tool_directory__}/tximport.R'
29 --format $input_source_selector.input_source
30 #if $input_source_selector.input_source == 'none':
31 --txIdCol '$input_source_selector.tx_id_col'
32 --abundanceCol '$input_source_selector.abundance_col'
33 --countsCol '$input_source_selector.counts_col'
34 --lengthCol '$input_source_selector.length_col'
35 #end if
36 #if $gene_id_source_selector.gene_id_source == 'gene_id_column_option':
37 --geneIdCol '$gene_id_source_selector.gene_id_column'
38 #else
39 #if $gene_id_source_selector.gff_source_selector.gff_source == "history":
40 #if $gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.mapping_file_option == 'tx2gene':
41 --tx2gene mapping.tab
42 #else
43 --gff_file mapping.gff
44 #end if
45 #else:
46 --tx2gene $gene_id_source_selector.gff_source_selector.tx2gene.fields.path
47 #end if
48 #end if
49 --countsFiles '$counts_files_table'
50 --countsFromAbundance $counts_from_abundance
51 --out_file '${gene_level_values}'
52 ]]></command>
53
54 <configfiles>
55 <configfile name="counts_files_table"><![CDATA[#echo "sample_id\tpath\n"
56 #for $file in $counts_file:
57 #echo str($file.element_identifier) + "\t" + str($file) + "\n"
58 #end for]]></configfile>
59 </configfiles>
60 <inputs>
61 <param name="counts_file" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
62 <conditional name="input_source_selector">
63 <param name="input_source" type ="select" label="Select the source of the quantification file">
64 <option value="salmon" selected="True">Salmon</option>
65 <option value="sailfish">Sailfish</option>
66 <option value="alevin">Alevin</option>
67 <option value="kallisto">Kallisto</option>
68 <option value="rsem">RSEM</option>
69 <option value="stringtie">Stringtie</option>
70 <option value="none">Custom format (specify the columns)</option>
71 </param>
72 <when value="none">
73 <param name="tx_id_col" type="text" label="Name of the txID columns"/>
74 <param name="abundance_col" type="text" label="Name of the abundance column"/>
75 <param name="counts_col" type="text" label="Name of the counts column"/>
76 <param name="length_col" type="text" label="Name of the length column"/>
77 </when>
78 <when value="salmon"/>
79 <when value="sailfish"/>
80 <when value="alevin"/>
81 <when value="kallisto"/>
82 <when value="rsem"/>
83 <when value="stringtie"/>
84 </conditional>
85 <conditional name="gene_id_source_selector" >
86 <param name="gene_id_source" type="select" label="Is the gene id part of the counts file or will be obtained from an external file?">
87 <option value="external_file" selected="True">Use an external file to map transcript to gene ids</option>
88 <option value="gene_id_column_option">Gene id is a column of the input file</option>
89 </param>
90 <when value="gene_id_column_option">
91 <param name="gene_id_column" type="text" label="Name of the column containing the geneID"/>
92 </when>
93 <when value="external_file">
94 <conditional name="gff_source_selector">
95 <param name="gff_source" type="select" label="Select a tx-to-gene table/GFF from your history or use a built-in file?">
96 <option value="built-in" selected="True">Use a built-in file</option>
97 <option value="history" >Use one from the history</option>
98 </param>
99 <when value="built-in">
100 <param name="tx2gene" type="select" label="Select an annotation version" help="If the build of your interest is not listed contact your Galaxy admin">
101 <options from_data_table="tx2gene_table">
102 <filter type="sort_by" column="1"/>
103 <validator type="no_options" message="No files are available for the selected input dataset"/>
104 </options>
105 </param>
106 </when>
107 <when value="history">
108 <conditional name="gff_tx2gene_selector">
109 <param name="mapping_file_option" type="select" label="Will you provide a tx2gene or a GFF/GTF file?">
110 <option value="tx2gene" selected="True">TranscriptID to GeneID table</option>
111 <option value="gff_gtf">GTF/GFF file</option>
112 </param>
113 <when value="gff_gtf">
114 <param name="own_gff" type="data" format="gff" label="Select your GFF file"/>
115 </when>
116 <when value="tx2gene">
117 <param name="own_tx2gene" type="data" format="tabular" label="Select your TranscriptID to GeneID table file"/>
118 </when>
119 </conditional>
120 </when>
121 </conditional>
122 </when>
123 </conditional>
124 <param name="counts_from_abundance" type="select" label="Summarization using the abundance (TPM) values?">
125 <option value="no">No</option>
126 <option value="scaled_TPM">Scaled up to library size</option>
127 <option value="length_scaled_TPM">Scaled using the avg. transcript legth over samples and then the library size</option>
128 <option value="dtu_scaled_TPM">Scaled using the median transcript length among isoforms of a gene, and then the library size</option>
129 </param>
130 </inputs>
131 <outputs>
132 <data name="gene_level_values" format="tabular" label="Gene level summarization on ${on_string}"/>
133 </outputs>
134
135 <tests>
136 <test>
137 <param name="input_source" value="salmon"/>
138 <param name="gene_id_source" value="external_file"/>
139 <param name="counts_from_abundance" value="no"/>
140 <param name="gff_source" value="history"/>
141 <param name="mapping_file_option" value="tx2gene"/>
142 <param name="own_tx2gene" value="tx2gene.tab"/>
143 <param name="counts_file" value="salmon_sample2.tab,salmon_sample1.tab" />
144 <output name="gene_level_values">
145 <assert_contents>
146 <has_text_matching expression="salmon_sample2.tab\tsalmon_sample1.tab" />
147 <has_text_matching expression="AT1G01010\t156\t156" />
148 </assert_contents>
149 </output>
150 </test>
151 <test>
152 <param name="input_source" value="salmon"/>
153 <param name="gene_id_source" value="external_file"/>
154 <param name="counts_from_abundance" value="no"/>
155 <param name="gff_source" value="history"/>
156 <param name="mapping_file_option" value="gff_gtf"/>
157 <param name="own_gff" value="Araport11_subset.gff3"/>
158 <param name="counts_file" value="salmon_sample2.tab,salmon_sample1.tab" />
159 <output name="gene_level_values">
160 <assert_contents>
161 <has_text_matching expression="salmon_sample2.tab\tsalmon_sample1.tab" />
162 <has_text_matching expression="AT1G01010\t156\t156" />
163 </assert_contents>
164 </output>
165 </test>
166 <test>
167 <param name="input_source" value="salmon"/>
168 <param name="gene_id_source" value="external_file"/>
169 <param name="counts_from_abundance" value="no"/>
170 <param name="gff_source" value="built-in"/>
171 <param name="tx2gene" value="Ath_Araport11_subset"/>
172 <param name="counts_file" value="salmon_sample2.tab,salmon_sample1.tab" />
173 <output name="gene_level_values">
174 <assert_contents>
175 <has_text_matching expression="salmon_sample2.tab\tsalmon_sample1.tab" />
176 <has_text_matching expression="AT1G01010\t156\t156" />
177 </assert_contents>
178 </output>
179 </test>
180 <!-- Test input with custom format -->
181 <test>
182 <param name="input_source" value="none"/>
183 <param name="tx_id_col" value="Transcript_id_here"/>
184 <param name="abundance_col" value="Abundance_goes_here"/>
185 <param name="counts_col" value="Here_goes_the_counts"/>
186 <param name="length_col" value="Here_goes_the_length"/>
187 <param name="counts_from_abundance" value="no"/>
188 <param name="gff_source" value="built-in"/>
189 <param name="tx2gene" value="Ath_Araport11_subset"/>
190 <param name="counts_file" value="custom_sample.tab" />
191 <output name="gene_level_values">
192 <assert_contents>
193 <has_text_matching expression="custom_sample.tab" />
194 <has_text_matching expression="AT1G01010\t156" />
195 </assert_contents>
196 </output>
197 </test>
198 </tests>
199 <help><![CDATA[
200 .. class:: infomark
201
202 Current version only works in 'merge' mode: A single table of gene summarizations is generated with one column for each sample file.
203 Take into account that DEseq2 package in Galaxy requires one table per sample.
204 ]]></help>
205 <citations>
206 <citation type="doi">doi:10.18129/B9.bioc.tximport</citation>
207 </citations>
208 </tool>