Mercurial > repos > iuc > chira_extract
comparison chira_extract.xml @ 5:dea6bc47a47e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
author | iuc |
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date | Fri, 20 Mar 2020 05:04:28 -0400 |
parents | 061844f6837f |
children | 56b2d956a1a6 |
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4:d129b3dfd2b8 | 5:dea6bc47a47e |
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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 |