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comparison groot.xml @ 3:0328139912c8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 90b5334805ccaec1ede5dc1b25a2b45d772a69f8
author iuc
date Wed, 08 Jan 2025 15:35:51 +0000
parents 54231cd54989
children
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2:54231cd54989 3:0328139912c8
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@">1</token> 5 <token name="@VERSION_SUFFIX@">2</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>
33 --minKmerCov $minKmerCov 33 --minKmerCov $minKmerCov
34 $noAlign 34 $noAlign
35 --processors "\${GALAXY_SLOTS:-1}" 35 --processors "\${GALAXY_SLOTS:-1}"
36 36
37 | groot report 37 | groot report
38 #if str($coverage.mode) == "cutoff"
38 --covCutoff '$covCutoff' 39 --covCutoff '$covCutoff'
39 $lowCov 40 #elif str($coverage.mode) == "lowcov"
41 --lowCov
42 #end if
40 > '$report_out' 43 > '$report_out'
41 44
42 ]]></command> 45 ]]></command>
43 <inputs> 46 <inputs>
44 <param argument="--fastq" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ file(s) to align"/> 47 <param argument="--fastq" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ file(s) to align"/>
56 <param argument="--sketchSize" type="integer" min="0" value="21" label="Size of MinHash sketch" /> 59 <param argument="--sketchSize" type="integer" min="0" value="21" label="Size of MinHash sketch" />
57 </section> 60 </section>
58 <section name="align" title="Align"> 61 <section name="align" title="Align">
59 <param argument="--contThresh" type="float" min="0" max="1.0" value="0.99" label="Containment threshold for the LSH ensemble" /> 62 <param argument="--contThresh" type="float" min="0" max="1.0" value="0.99" label="Containment threshold for the LSH ensemble" />
60 <param argument="--minKmerCov" type="integer" min="0" value="1" label="Minimum number of k-mers covering each base of a graph segment" /> 63 <param argument="--minKmerCov" type="integer" min="0" value="1" label="Minimum number of k-mers covering each base of a graph segment" />
61 <param argument="--noAlign" type="boolean" truevalue="" falsevalue="--noAlign" label="Perform exact alignment?" 64 <param argument="--noAlign" type="boolean" checked="true" truevalue="" falsevalue="--noAlign" label="Perform exact alignment?"
62 help="If not, graphs will still be weighted using approximate read mappings"/> 65 help="If 'No', --noAlign will be set, no exact alignment will be performed and graphs will still be weighted using approximate read mappings"/>
63 </section> 66 </section>
64 <section name="report" title="Report"> 67 <section name="report" title="Report">
65 <param argument="--covCutoff" type="float" min="0" max="1.0" value="0.97" label="Coverage cutoff for reporting ARGs" /> 68 <conditional name="coverage">
66 <param argument="--lowCov" type="boolean" checked="false" truevalue="--lowCov" falsevalue="" label="Report ARGs which may not be covered at the 5'/3' ends" 69 <param name="mode" type="select" label="Choose your coverage mode" help="" >
67 help="If 'Yes', overrides --covCutoff option"/> 70 <option value="cutoff" selected="true">Choose your coverage cutoff</option>
71 <option value="lowcov">Low coverage (will report ARGs which may not be covered at the 5’/3’ ends)</option>
72 </param>
73 <when value="cutoff">
74 <param argument="--covCutoff" type="float" min="0" max="1.0" value="0.97" label="Coverage cutoff for reporting ARGs" />
75 </when>
76 <when value="lowcov"/>
77 </conditional>
68 </section> 78 </section>
69 </inputs> 79 </inputs>
70 <outputs> 80 <outputs>
71 <data name="report_out" format="tabular" label="${tool.name} on ${on_string}: Report"/> 81 <data name="report_out" format="tabular" label="${tool.name} on ${on_string}: Report"/>
72 </outputs> 82 </outputs>
83 <param name="sketchSize" value="20"/> 93 <param name="sketchSize" value="20"/>
84 </section> 94 </section>
85 <section name="align"> 95 <section name="align">
86 <param name="contThresh" value="0.99"/> 96 <param name="contThresh" value="0.99"/>
87 <param name="minKmerCov" value="1" /> 97 <param name="minKmerCov" value="1" />
88 <param name="noAlign" value=""/>
89 </section> 98 </section>
90 <section name="report"> 99 <section name="report">
91 <conditional name="arg_report"> 100 <conditional name="coverage">
92 <param name="criteria" value="cutoff" /> 101 <param name="mode" value="cutoff"/>
93 <param name="covCutoff" value="0.97" /> 102 <param name="covCutoff" value="0.97" />
94 </conditional> 103 </conditional>
95 </section> 104 </section>
96 <output name="report_out" ftype="tabular"> 105 <output name="report_out" ftype="tabular">
97 <assert_contents> 106 <assert_contents>
113 <param name="sketchSize" value="21"/> 122 <param name="sketchSize" value="21"/>
114 </section> 123 </section>
115 <section name="align"> 124 <section name="align">
116 <param name="contThresh" value="0.99"/> 125 <param name="contThresh" value="0.99"/>
117 <param name="minKmerCov" value="1" /> 126 <param name="minKmerCov" value="1" />
118 <param name="noAlign" value=""/> 127 <param name="noAlign" value="true"/>
119 </section> 128 </section>
120 <section name="report"> 129 <section name="report">
121 <param name="covCutoff" value="0.97" /> 130 <conditional name="coverage">
122 <param name="lowCov" value="True"/> 131 <param name="mode" value="lowcov"/>
132 </conditional>
123 </section> 133 </section>
124 <output name="report_out" ftype="tabular"> 134 <output name="report_out" ftype="tabular">
125 <assert_contents> 135 <assert_contents>
126 <has_text text="argannot~~~(Bla)VIM-9~~~AY524988:1-801"/> 136 <has_text text="argannot~~~(Bla)VIM-9~~~AY524988:1-801"/>
127 <has_text text="argannot~~~(Bla)VIM-20~~~GQ414736:1-801"/> 137 <has_text text="argannot~~~(Bla)VIM-20~~~GQ414736:1-801"/>