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comparison groot.xml @ 1:eea643713525 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit fcdb311680cae04b0d4f002a39abcbf338d7de41
author iuc
date Thu, 14 Nov 2024 15:40:22 +0000
parents fbe36cf83eb7
children 54231cd54989
comparison
equal deleted inserted replaced
0:fbe36cf83eb7 1:eea643713525
1 <tool id="groot" name="Groot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="groot" name="Groot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> align reads to references and weight variation graphs and generate report</description> 2 <description> align reads to references and weight variation graphs and generate report</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.1.2</token> 4 <token name="@TOOL_VERSION@">1.1.2</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 <token name="@PROFILE@">22.05</token> 6 <token name="@PROFILE@">22.05</token>
7 </macros> 7 </macros>
8 <xrefs> 8 <xrefs>
9 <xref type="bio.tools">groot</xref> 9 <xref type="bio.tools">groot</xref>
10 </xrefs> 10 </xrefs>
11 <requirements> 11 <requirements>
12 <requirement type="package" version="@TOOL_VERSION@">groot</requirement> 12 <requirement type="package" version="@TOOL_VERSION@">groot</requirement>
13 </requirements> 13 </requirements>
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 set -x pipefail; 15 set -x pipefail;
16 #set $extension = str($fastq.ext) 16 #set $extension = "fastq.gz" if str($fastq.ext).endswith(".gz") else "fastq"
17 ln -s -f '${fastq}' 'input.${extension}' && 17 ln -s -f '${fastq}' 'input.${extension}' &&
18 groot index 18 groot index
19 --msaDir '$groot_db_select.fields.path' 19 --msaDir '$groot_db_select.fields.path'
20 --indexDir 'grootIndex' 20 --indexDir 'grootIndex'
21 --windowSize $windowSize 21 --windowSize $windowSize
29 groot align 29 groot align
30 --fastq 'input.${extension}' 30 --fastq 'input.${extension}'
31 --indexDir 'grootIndex' 31 --indexDir 'grootIndex'
32 --contThresh $contThresh 32 --contThresh $contThresh
33 --minKmerCov $minKmerCov 33 --minKmerCov $minKmerCov
34 --log '$log'
35 $noAlign 34 $noAlign
36 --processors "\${GALAXY_SLOTS:-1}" 35 --processors "\${GALAXY_SLOTS:-1}"
37 36
38 | groot report 37 | groot report
39 --covCutoff '$covCutoff' 38 --covCutoff '$covCutoff'
67 <param argument="--lowCov" type="boolean" checked="false" truevalue="--lowCov" falsevalue="" label="Report ARGs which may not be covered at the 5'/3' ends" 66 <param argument="--lowCov" type="boolean" checked="false" truevalue="--lowCov" falsevalue="" label="Report ARGs which may not be covered at the 5'/3' ends"
68 help="If 'Yes', overrides --covCutoff option"/> 67 help="If 'Yes', overrides --covCutoff option"/>
69 </section> 68 </section>
70 </inputs> 69 </inputs>
71 <outputs> 70 <outputs>
72 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/>
73 <data name="report_out" format="tabular" label="${tool.name} on ${on_string}: Report"/> 71 <data name="report_out" format="tabular" label="${tool.name} on ${on_string}: Report"/>
74 </outputs> 72 </outputs>
75 <tests> 73 <tests>
76 <test expect_num_outputs="2"> 74 <test expect_num_outputs="1">
77 <param name="fastq" value="bla-b7-150bp-5x.fq" ftype="fastq"/> 75 <param name="fastq" value="bla-b7-150bp-5x.fq" ftype="fastq"/>
78 <section name="index"> 76 <section name="index">
79 <param name="groot_db_select" value="resfinder.90" /> 77 <param name="groot_db_select" value="resfinder.90" />
80 <param name="windowSize" value="150"/> 78 <param name="windowSize" value="150"/>
81 <param name="kmerSize" value="31"/> 79 <param name="kmerSize" value="31"/>
100 <has_text text="blaB-7_1_AF189304"/> 98 <has_text text="blaB-7_1_AF189304"/>
101 <has_n_lines n="1"/> 99 <has_n_lines n="1"/>
102 <has_n_columns n="4"/> 100 <has_n_columns n="4"/>
103 </assert_contents> 101 </assert_contents>
104 </output> 102 </output>
105 <output name="log" ftype="txt">
106 <assert_contents>
107 <has_text text="version"/>
108 <has_text text="1.1.2"/>
109 </assert_contents>
110 </output>
111 </test> 103 </test>
112 <test expect_num_outputs="2"> 104 <test expect_num_outputs="1">
113 <param name="fastq" value="argannot_light-150bp-10000-reads.fq.gz" ftype="fastq.gz"/> 105 <param name="fastq" value="argannot_light-150bp-10000-reads.fq.gz" ftype="fastq.gz"/>
114 <section name="index"> 106 <section name="index">
115 <param name="groot_db_select" value="arg-annot.90" /> 107 <param name="groot_db_select" value="arg-annot.90" />
116 <param name="windowSize" value="150"/> 108 <param name="windowSize" value="150"/>
117 <param name="kmerSize" value="41"/> 109 <param name="kmerSize" value="41"/>
133 <assert_contents> 125 <assert_contents>
134 <has_text text="argannot~~~(Bla)VIM-9~~~AY524988:1-801"/> 126 <has_text text="argannot~~~(Bla)VIM-9~~~AY524988:1-801"/>
135 <has_text text="argannot~~~(Bla)VIM-20~~~GQ414736:1-801"/> 127 <has_text text="argannot~~~(Bla)VIM-20~~~GQ414736:1-801"/>
136 <has_n_lines n="5"/> 128 <has_n_lines n="5"/>
137 <has_n_columns n="4"/> 129 <has_n_columns n="4"/>
138 </assert_contents>
139 </output>
140 <output name="log" ftype="txt">
141 <assert_contents>
142 <has_text text="version"/>
143 <has_text text="1.1.2"/>
144 </assert_contents> 130 </assert_contents>
145 </output> 131 </output>
146 </test> 132 </test>
147 </tests> 133 </tests>
148 <help><![CDATA[ 134 <help><![CDATA[