|
0
|
1 <tool id="pvac-seq" name="PVAC-seq" version="0.1.0">
|
|
|
2 <command detect_errors="exit_code"><![CDATA[
|
|
|
3 #if str( $epitope_length ) != "":
|
|
|
4 #set $epitope_length = "-e " + str($epitope_length)
|
|
|
5 #end if
|
|
|
6 #set algs = ' '.join([str($alg) for $alg in $algorithms])
|
|
|
7 pvacseq run
|
|
|
8 ${epitope_length}
|
|
3
|
9 --iedb-install-directory "\$IEDB_INSTALL_DIRECTORY"
|
|
0
|
10 --tdna-vaf ${tdna_vaf}
|
|
|
11 --net-chop-method ${net_chop_method}
|
|
|
12 ${net_mhc_stab}
|
|
|
13 --top-score-metric ${top_score_metric}
|
|
|
14 --downstream-sequence-length ${downstream_sequence_length}
|
|
|
15 ${input_vcf}
|
|
|
16 galaxy
|
|
|
17 ${allele}
|
|
|
18 ${algs}
|
|
4
|
19 `pwd` &&
|
|
|
20 mv combined/galaxy.filtered.tsv ${output_filtered} &&
|
|
|
21 mv combined/galaxy.all_epitopes.tsv ${output_all}
|
|
0
|
22
|
|
|
23 ]]></command>
|
|
|
24 <inputs>
|
|
|
25 <param type="data" name="input_vcf" format="vcf" />
|
|
|
26 <param type="text" name="allele" />
|
|
|
27 <param name="algorithms" type="select" multiple="true" label="Epitope prediction algorithms">
|
|
|
28 <option value="NNalign">NNalign</option>
|
|
|
29 <option value="NetMHC">NetMHC</option>
|
|
|
30 <option value="NetMHCIIpan">NetMHCIIpan</option>
|
|
|
31 <option value="NetMHCcons">NetMHCcons</option>
|
|
|
32 <option value="NetMHCpan">NetMHCpan</option>
|
|
|
33 <option value="PickPocket">PickPocket</option>
|
|
|
34 <option value="SMMPMBEC">SMMPMBEC</option>
|
|
|
35 <option value="SMMalign">SMMalign</option>
|
|
|
36 </param>
|
|
|
37
|
|
|
38 <param type="text" name="epitope_length"/>
|
|
|
39 <param type="text" name="downstream_sequence_length" value="1000" help="int or 'full'"/>
|
|
|
40 <param type="text" name="tdna_vaf" value="40"/>
|
|
|
41 <param name="net_chop_method" type="select" label="NetChop prediction method">
|
|
|
42 <option value="cterm">cterm</option>
|
|
|
43 <option value="20s">20S</option>
|
|
|
44 </param>
|
|
|
45 <param name="net_mhc_stab" type="select" label="Run NetMHCStabPan after all filtering?">
|
|
|
46 <option value="--netmhc-stab">Yes</option>
|
|
|
47 <option value="">No</option>
|
|
|
48 </param>
|
|
|
49 <param name="top_score_metric" type="select" label="The ic50 scoring metric to use">
|
|
|
50 <option value="median">Median</option>
|
|
|
51 <option value="lowest">Lowest</option>
|
|
|
52 </param>
|
|
|
53 </inputs>
|
|
|
54 <outputs>
|
|
4
|
55 <data name="output_all" format="tabular"/>
|
|
|
56 <data name="output_filtered" format="tabular"/>
|
|
0
|
57 </outputs>
|
|
|
58 <help><![CDATA[
|
|
|
59 TODO: Fill in help.
|
|
|
60 ]]></help>
|
|
|
61 </tool> |
