Mercurial > repos > iuc > chira_extract

comparison chira_extract.xml @ 11:a618f28e1496 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 51f68a6d51d9e87f8e54021ce760b1506a3589b8"
author iuc
date Sun, 14 Jun 2020 17:37:05 -0400
parents 7ec1d063fecd
children 97ca48f470ef
comparison
equal deleted inserted replaced
10:7ec1d063fecd 11:a618f28e1496
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 34 $seed_interaction
35 -sbp '$seed_bp'
36 -smpu '$seed_min_pu'
37 -acc '$accessibility'
38 -accw '$acc_width'
39 -m '$intarna_mode'
35 $summarize 40 $summarize
36 -a '$accessibility'
37 -m '$intarna_mode'
38 -p "\${GALAXY_SLOTS:-2}" 41 -p "\${GALAXY_SLOTS:-2}"
39 -o ./ 42 -o ./
40 ]]></command> 43 ]]></command>
41 44
42 <inputs> 45 <inputs>
91 </when> 94 </when>
92 </conditional> 95 </conditional>
93 <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" 96 <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"
94 label="Hybridize chimeric loci?" 97 label="Hybridize chimeric loci?"
95 help="Turning this option on increases the run time of the tool significantly."/> 98 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"> 99 <param name="intarna_mode" type="select">
101 <option value="H">Heuristic</option> 100 <option value="H">Heuristic</option>
102 <option value="M">Exact</option> 101 <option value="M">Exact</option>
103 <option value="S">Seed-only</option> 102 <option value="S">Seed-only</option>
104 </param> 103 </param>
104 <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--noSeed" checked="true"
105 label="Enforce seed interaction?"/>
106 <param name="seed_bp" type="integer" value="5" min="2" max="20"
107 label="Number of inter-molecular base pairs within the seed region"
108 help="IntaRNA --seedBP parameter"/>
109 <param name="seed_min_pu" type="float" value="0" min="0" max="1"
110 label="Minimal unpaired probability (per sequence) a seed region may have"
111 help="IntaRNA --seedMinPu parameter"/>
112 <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"
113 label="Compute accessibility profiles for interacting sequences?"/>
114 <param name="acc_width" type="integer" value="150" min="0" max="99999"
115 label="Sliding window size for accessibility computation"
116 help="IntaRNA --accW parameter"/>
117 <param name="temperature" type="float" value="37" min="0" max="100"
118 label="IntaRNA temperature parameter in Celsius to setup the VRNA energy parameters"/>
105 <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false" 119 <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"
106 label="Summarize interactions at loci level?"/> 120 label="Summarize interactions at loci level?"/>
107 </inputs> 121 </inputs>
108 122
109 <outputs> 123 <outputs>
110 <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/> 124 <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric 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}"> 125 <data format="tabular" name="interactions" from_work_dir="interactions" label="ChiRA interaction summary on ${on_string}">
113 <filter>summarize == True</filter> 126 <filter>summarize == True</filter>
114 </data> 127 </data>
115 </outputs> 128 </outputs>
116 129
117 <tests> 130 <tests>
118 <test expect_num_outputs="3"> 131 <test expect_num_outputs="2">
119 <param name="loci" value="loci.counts"/> 132 <param name="loci" value="loci.counts"/>
120 <param name="ref_type" value="split"/> 133 <param name="ref_type" value="split"/>
121 <param name="ref_fasta1" value="ref1.fasta"/> 134 <param name="ref_fasta1" value="ref1.fasta"/>
122 <param name="ref_fasta2" value="ref2.fasta"/> 135 <param name="ref_fasta2" value="ref2.fasta"/>
123 <param name="annot_choice" value="no"/> 136 <param name="annot_choice" value="no"/>
124 <param name="hybridize" value="true" /> 137 <param name="hybridize" value="true" />
125 <param name="summarize" value="true" /> 138 <param name="summarize" value="true" />
126 <output name="chimeras" file="chimeras"/> 139 <output name="chimeras" file="chimeras"/>
127 <output name="singletons" file="singletons"/>
128 <output name="interactions" file="interactions"/> 140 <output name="interactions" file="interactions"/>
129 </test> 141 </test>
130 </tests> 142 </tests>
131 <help> 143 <help>
132 144