Mercurial > repos > iuc > colibread_lordec

comparison lordec.xml @ 7:552041078feb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
author iuc
date Sat, 05 Oct 2024 19:53:50 +0000
parents 434af4cbf682
children
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6:434af4cbf682 7:552041078feb
1 <tool id="lordec" name="Lordec" version="0.9+galaxy2" profile="@PROFILE@"> 1 <tool id="lordec" name="Lordec" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
2 <description>is a set a programs for correcting sequencing errors in PacBio reads</description> 2 <description>is a set a programs for correcting sequencing errors in PacBio reads</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.9</token>
4 <import>macros.xml</import> 5 <import>macros.xml</import>
5 </macros> 6 </macros>
6 <requirements> 7 <requirements>
7 <requirement type="package" version="0.9">lordec</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">lordec</requirement>
8 </requirements> 9 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 #if str( $program_type_choice.program_type ) == "correct": 11 #if str( $program_type_choice.program_type ) == "correct":
11 lordec-correct 12 lordec-correct
12 @lordec_inputs@ 13 @lordec_inputs@
61 <expand macro="lordec_inputs" /> 62 <expand macro="lordec_inputs" />
62 </when> 63 </when>
63 </conditional> 64 </conditional>
64 </inputs> 65 </inputs>
65 <outputs> 66 <outputs>
66 <data format="fasta" name="corrected_read_file" label="Corrected long reads with ${tool.name} on ${on_string}" > 67 <data format="fasta" name="corrected_read_file" label="${tool.name} on ${on_string}: Corrected long reads" >
67 <filter>program_type_choice['program_type'] == 'correct'</filter> 68 <filter>program_type_choice['program_type'] == 'correct'</filter>
68 </data> 69 </data>
69 <data format="fasta" name="trimmed_reads_file" label="Trimmed reads file with ${tool.name} on ${on_string}" > 70 <data format="fasta" name="trimmed_reads_file" label="${tool.name} on ${on_string}: Trimmed reads" >
70 <filter>program_type_choice['program_type'] == 'trim'</filter> 71 <filter>program_type_choice['program_type'] == 'trim'</filter>
71 </data> 72 </data>
72 <data format="tabular" name="stat_file" label="Stats with ${tool.name} on ${on_string}" > 73 <data format="tabular" name="stat_file" label="${tool.name} on ${on_string}: Stats" >
73 <filter>program_type_choice['program_type'] == 'stats'</filter> 74 <filter>program_type_choice['program_type'] == 'stats'</filter>
74 </data> 75 </data>
75 </outputs> 76 </outputs>
76 <tests> 77 <tests>
77 <test> 78 <test expect_num_outputs="1">
78 <conditional name="program_type_choice"> 79 <conditional name="program_type_choice">
79 <param name="program_type" value="correct" /> 80 <param name="program_type" value="correct" />
80 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" ftype="fasta.gz"/> 81 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" ftype="fasta.gz"/>
81 <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" /> 82 <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" />
82 <param name="k" value="31" /> 83 <param name="k" value="31" />
83 </conditional> 84 </conditional>
84 <output name="corrected_read_file" file="lordec/corrected_reads.fa"/> 85 <output name="corrected_read_file" file="lordec/corrected_reads.fa"/>
85 </test> 86 </test>
86 <test> 87 <test expect_num_outputs="1">
87 <conditional name="program_type_choice"> 88 <conditional name="program_type_choice">
88 <param name="program_type" value="trim" /> 89 <param name="program_type" value="trim" />
89 <param name="i" value="lordec/corrected_reads.fa" ftype="fasta"/> 90 <param name="i" value="lordec/corrected_reads.fa" ftype="fasta"/>
90 </conditional> 91 </conditional>
91 <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/> 92 <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/>
92 </test> 93 </test>
93 <test> 94 <test expect_num_outputs="1">
94 <conditional name="program_type_choice"> 95 <conditional name="program_type_choice">
95 <param name="program_type" value="stats" /> 96 <param name="program_type" value="stats" />
96 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" /> 97 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" />
97 <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" /> 98 <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" />
98 </conditional> 99 </conditional>