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comparison seq2hla.xml @ 3:2e2130c69672 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
author iuc
date Tue, 07 Mar 2023 13:10:11 +0000
parents 62423040f17e
children
comparison
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2:62423040f17e 3:2e2130c69672
1 <tool id="seq2hla" name="seq2HLA" version="2.2.0+galaxy1"> 1 <tool id="seq2hla" name="seq2HLA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>HLA genotype and expression from RNA-seq</description> 2 <description>HLA genotype and expression from RNA-seq</description>
3 <macros>
4 <token name="@TOOL_VERSION@">2.3</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
3 <xrefs> 7 <xrefs>
4 <xref type="bio.tools">seq2hla</xref> 8 <xref type="bio.tools">seq2hla</xref>
5 </xrefs> 9 </xrefs>
6 <requirements> 10 <requirements>
7 <!-- needed because of some non POSIX compliant wc usage --> 11 <requirement type="package" version="@TOOL_VERSION@">seq2hla</requirement>
8 <requirement type="package" version="8.31">coreutils</requirement>
9 <requirement type="package" version="2.2">seq2hla</requirement>
10 </requirements> 12 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
12 seq2HLA --runName='$run_name' -1 '$fastq_input1' -2 '$fastq_input2' 14 seq2HLA --runName='$run_name'
15 #if str( $fastq_input.fastq_input_selector ) == "paired":
16 -1 '${fastq_input.fastq_input1}'
17 -2 '${fastq_input.fastq_input2}'
18 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
19 -1 '${fastq_input.fastq_input1.forward}'
20 -2 '${fastq_input.fastq_input1.reverse}'
21 #end if
13 #if str($trim) != '': 22 #if str($trim) != '':
14 --trim3=$trim 23 --trim3=$trim
15 #end if 24 #end if
16 -p \${GALAXY_SLOTS:-1} >> '$seq2hla_log' 25 -p \${GALAXY_SLOTS:-1} >> '$seq2hla_log'
17 && cp -p '${run_name}-ClassI.HLAgenotype2digits' '${c1_genotype2digits}' 26 && cp -p '${run_name}-ClassI-class.HLAgenotype2digits' '${c1_genotype2digits}'
18 && cp -p '${run_name}-ClassI.HLAgenotype4digits' '${c1_genotype4digits}' 27 && cp -p '${run_name}-ClassI-class.HLAgenotype4digits' '${c1_genotype4digits}'
19 && echo '#Locus_RPKM' | cat - '${run_name}-ClassI.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c1_expression}' 28 && echo '#Locus_RPKM' | cat - '${run_name}-ClassI-class.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c1_expression}'
20 && cp -p '${run_name}-ClassII.HLAgenotype4digits' '${c2_genotype4digits}' 29 && cp -p '${run_name}-ClassII.HLAgenotype4digits' '${c2_genotype4digits}'
21 && echo '#Locus_RPKM' | cat - '${run_name}-ClassII.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c2_expression}' 30 && echo '#Locus_RPKM' | cat - '${run_name}-ClassII.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c2_expression}'
22 && cp -p '${run_name}.ambiguity' '${ambiguity}' 31 && cp -p '${run_name}.ambiguity' '${ambiguity}'
23 ]]></command> 32 ]]></command>
24 <inputs> 33 <inputs>
25 <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis"> 34 <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis">
26 <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator> 35 <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator>
27 </param> 36 </param>
28 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> 37 <conditional name="fastq_input">
29 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/> 38 <param name="fastq_input_selector" type="select" label="Paired-end reads" help="Select between paired and paired-collection data">
39 <option value="paired">Paired</option>
40 <option value="paired_collection">Paired Collection</option>
41 </param>
42 <when value="paired">
43 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
44 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
45 </when>
46 <when value="paired_collection">
47 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a collection of paired-end reads"/>
48 </when>
49 </conditional>
30 <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime" 50 <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime"
31 help="trim this many bases from the low-quality end of each read" /> 51 help="trim this many bases from the low-quality end of each read" />
32 </inputs> 52 </inputs>
33 <outputs> 53 <outputs>
34 <data format="txt" name="seq2hla_log" label="${tool.name} on ${on_string}: ${run_name} logfile"/> 54 <data format="txt" name="seq2hla_log" label="${tool.name} on ${on_string}: ${run_name} logfile"/>
35 <data format="tabular" name="c1_genotype2digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype2digits"/> 55 <data format="tabular" name="c1_genotype2digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype2digits"/>
36 <data format="tabular" name="c1_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype4digits"/> 56 <data format="tabular" name="c1_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype4digits"/>
37 <data format="tabular" name="c2_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassII.HLAgenotype4digits"/> 57 <data format="tabular" name="c2_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassII.HLAgenotype4digits"/>
38 <data format="tabular" name="c1_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassI.expression"/> 58 <data format="tabular" name="c1_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassI.expression"/>
39 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/> 59 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/>
40 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/>
41 <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/> 60 <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/>
42 </outputs> 61 </outputs>
43 <tests> 62 <tests>
44 <test> 63 <test>
45 <param name="run_name" value="test"/> 64 <param name="run_name" value="test"/>
46 <param name="fastq_input1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/> 65 <conditional name="fastq_input">
47 <param name="fastq_input2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/> 66 <param name="fastq_input_selector" value="paired"/>
67 <param name="fastq_input1" ftype="fastqsanger" value="reads1.fastq"/>
68 <param name="fastq_input2" ftype="fastqsanger" value="reads2.fastq"/>
69 </conditional>
70 <output name="c1_genotype4digits">
71 <assert_contents>
72 <has_text text="A*24:02" />
73 </assert_contents>
74 </output>
75 </test>
76 <test>
77 <param name="run_name" value="test_collection"/>
78 <conditional name="fastq_input">
79 <param name="fastq_input_selector" value="paired_collection"/>
80 <param name="fastq_input1">
81 <collection type="paired">
82 <element name="forward" ftype="fastqsanger" value="reads1.fastq" />
83 <element name="reverse" ftype="fastqsanger" value="reads2.fastq" />
84 </collection>
85 </param>
86 </conditional>
48 <output name="c1_genotype4digits"> 87 <output name="c1_genotype4digits">
49 <assert_contents> 88 <assert_contents>
50 <has_text text="A*24:02" /> 89 <has_text text="A*24:02" />
51 </assert_contents> 90 </assert_contents>
52 </output> 91 </output>
98 B 139.66 137 B 139.66
99 C 184.42 138 C 184.42
100 ======= ====== 139 ======= ======
101 140
102 141
103 .. _seq2HLA: https://bitbucket.org/sebastian_boegel/seq2hla 142 .. _seq2HLA: https://github.com/TRON-Bioinformatics/seq2HLA
104 143
105 ]]></help> 144 ]]></help>
106 <citations> 145 <citations>
107 <citation type="doi">10.1186/gm403</citation> 146 <citation type="doi">10.1186/gm403</citation>
108 </citations> 147 </citations>