Mercurial > repos > iuc > chira_extract

comparison chira_extract.xml @ 9:56b2d956a1a6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
author iuc
date Fri, 29 May 2020 06:57:01 -0400
parents dea6bc47a47e
children 7ec1d063fecd
comparison
equal deleted inserted replaced
8:89ab3b2973d8 9:56b2d956a1a6
29 #else if str($reference.ref_type) == "split": 29 #else if str($reference.ref_type) == "split":
30 -f1 '$reference.ref_fasta1' 30 -f1 '$reference.ref_fasta1'
31 -f2 '$reference.ref_fasta2' 31 -f2 '$reference.ref_fasta2'
32 #end if 32 #end if
33 $hybridize 33 $hybridize
34 $seed_interaction
35 $summarize
36 -a '$accessibility'
37 -m '$intarna_mode'
34 -p "\${GALAXY_SLOTS:-2}" 38 -p "\${GALAXY_SLOTS:-2}"
35 -o ./ 39 -o ./
36 ]]></command> 40 ]]></command>
37 41
38 <inputs> 42 <inputs>
84 <when value="single"> 88 <when value="single">
85 <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file" 89 <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file"
86 help="Reference fasta file"/> 90 help="Reference fasta file"/>
87 </when> 91 </when>
88 </conditional> 92 </conditional>
89 <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" /> 93 <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"
94 label="Hybridize chimeric loci?"
95 help="Turning this option on increases the run time of the tool significantly."/>
96 <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--noSeed" checked="false"
97 label="Enforce seed interaction?"/>
98 <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"
99 label="Compute accessibility profiles for interacting sequences?"/>
100 <param name="intarna_mode" type="select">
101 <option value="H">Heuristic</option>
102 <option value="M">Exact</option>
103 <option value="S">Seed-only</option>
104 </param>
105 <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"
106 label="Summarize interactions at loci level?"/>
90 </inputs> 107 </inputs>
91 108
92 <outputs> 109 <outputs>
93 <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/> 110 <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/>
94 <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/> 111 <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/>
112 <data format="tabular" name="interactions" from_work_dir="interactions" label="ChiRA interaction summary on ${on_string}">
113 <filter>summarize == True</filter>
114 </data>
95 </outputs> 115 </outputs>
96 116
97 <tests> 117 <tests>
98 <test expect_num_outputs="2"> 118 <test expect_num_outputs="3">
99 <param name="loci" value="loci.counts"/> 119 <param name="loci" value="loci.counts"/>
100 <param name="ref_type" value="split"/> 120 <param name="ref_type" value="split"/>
101 <param name="ref_fasta1" value="ref1.fasta"/> 121 <param name="ref_fasta1" value="ref1.fasta"/>
102 <param name="ref_fasta2" value="ref2.fasta"/> 122 <param name="ref_fasta2" value="ref2.fasta"/>
103 <param name="annot_choice" value="no"/> 123 <param name="annot_choice" value="no"/>
104 <param name="hybridize" value="true" /> 124 <param name="hybridize" value="true" />
105 <output name="chimeras" file="chimeras" sort="True"/> 125 <param name="summarize" value="true" />
106 <output name="singletons" file="singletons" sort="True"/> 126 <output name="chimeras" file="chimeras"/>
127 <output name="singletons" file="singletons"/>
128 <output name="interactions" file="interactions"/>
107 </test> 129 </test>
108 </tests> 130 </tests>
109 <help> 131 <help>
110 132
111 .. class:: infomark 133 .. class:: infomark