Mercurial > repos > iuc > chira_extract

comparison chira_extract.xml @ 5:dea6bc47a47e 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 aafb8e5de9023eeddd7f4683909f418ef5aae086"
author iuc
date Fri, 20 Mar 2020 05:04:28 -0400
parents 061844f6837f
children 56b2d956a1a6
comparison
equal deleted inserted replaced
4:d129b3dfd2b8 5:dea6bc47a47e
23 #end if 23 #end if
24 -tc '$tpm_cutoff' 24 -tc '$tpm_cutoff'
25 -sc '$score_cutoff' 25 -sc '$score_cutoff'
26 -co '$chimeric_overlap' 26 -co '$chimeric_overlap'
27 #if str($reference.ref_type) == "single": 27 #if str($reference.ref_type) == "single":
28 -f1 '$ref_fasta' 28 -f1 '$reference.ref_fasta'
29 #else if str($reference.ref_type) == "split": 29 #else if str($reference.ref_type) == "split":
30 -f1 '$ref_fasta1' 30 -f1 '$reference.ref_fasta1'
31 -f2 '$ref_fasta2' 31 -f2 '$reference.ref_fasta2'
32 #end if 32 #end if
33 $hybridize 33 $hybridize
34 -p "\${GALAXY_SLOTS:-2}" 34 -p "\${GALAXY_SLOTS:-2}"
35 -o ./ 35 -o ./
36 ]]></command> 36 ]]></command>
37 37
60 </when> 60 </when>
61 </conditional> 61 </conditional>
62 </when> 62 </when>
63 <when value="no"> 63 <when value="no">
64 <!-- Do nothing --> 64 <!-- Do nothing -->
65 </when> 65 </when>
66 </conditional> 66 </conditional>
67 <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1" 67 <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1"
68 help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/> 68 help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/>
69 <param name="score_cutoff" type="float" value="0" label="Score cut-off" min="0" max="2" 69 <param name="score_cutoff" type="float" value="0" label="Score cut-off" min="0" max="2"
70 help="Hybrids with less than this score will be discarded in the final output. [0-2.0]"/> 70 help="Hybrids with less than this score will be discarded in the final output. [0-2.0]"/>
86 help="Reference fasta file"/> 86 help="Reference fasta file"/>
87 </when> 87 </when>
88 </conditional> 88 </conditional>
89 <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" /> 89 <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" />
90 </inputs> 90 </inputs>
91 91
92 <outputs> 92 <outputs>
93 <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/> 93 <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}"/> 94 <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/>
95 </outputs> 95 </outputs>
96 96
97 <tests> 97 <tests>
98 <test expect_num_outputs="2"> 98 <test expect_num_outputs="2">
99 <param name="loci" value="loci.counts"/> 99 <param name="loci" value="loci.counts"/>
100 <param name="ref_type" value="split"/> 100 <param name="ref_type" value="split"/>
101 <param name="ref_fasta1" value="ref1.fasta"/> 101 <param name="ref_fasta1" value="ref1.fasta"/>
110 110
111 .. class:: infomark 111 .. class:: infomark
112 112
113 **What it does** 113 **What it does**
114 114
115 This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to. 115 This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to.
116 116
117 **Inputs** 117 **Inputs**
118 118
119 * Tabular file containing CRLs information 119 * Tabular file containing CRLs information
120 * Annotation GTF file 120 * Annotation GTF file