Mercurial > repos > artbio > xpore

comparison xpore_dataprep.xml @ 1:ff53cf0d0bbd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
author artbio
date Fri, 28 May 2021 23:32:25 +0000
parents b64b9a2bf4f0
children a5758bb680c8
comparison
equal deleted inserted replaced
0:b64b9a2bf4f0 1:ff53cf0d0bbd
1 <tool id="xpore_dataprep" name="xpore-dataprep" version="0.5.6+galaxy1"> 1 <tool id="xpore_dataprep" name="xpore-dataprep" version="0.5.6+galaxy2">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.5.6">xpore</requirement> 4 <requirement type="package" version="0.5.6">xpore</requirement>
5 <requirement type="package" version="1.9.0">pyensembl</requirement>
6 </requirements> 5 </requirements>
7 <stdio> 6 <stdio>
8 <exit_code range="1:" level="fatal" description="Tool exception" /> 7 <exit_code range="1:" level="fatal" description="Tool exception" />
9 </stdio> 8 </stdio>
10 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
11 xpore-dataprep 10 xpore-dataprep
12 --eventalign '$eventalign_reads' 11 --eventalign '$eventalign_reads'
13 --summary '$eventalign_summary' 12 --summary '$eventalign_summary'
14 --out_dir out 13 --out_dir out
15 --n_processes \${GALAXY_SLOTS:-4} && 14 --n_processes \${GALAXY_SLOTS:-4} &&
16 ls -la out 15 mv ./out/data.index $data_index &&
16 mv ./out/eventalign.hdf5 $eventalign_hdf5 &&
17 mv ./out/data.log $data_log &&
18 mv ./out/eventalign.log $eventalign_log &&
19 mv ./out/data.readcount $data_readcount &&
20 mv ./out/data.json $data_json
21
22
17 ]]></command> 23 ]]></command>
18 <inputs> 24 <inputs>
19 <param name="eventalign_reads" type="data" format="txt,tabular" label="aligned nanopore events" 25 <param name="eventalign_reads" type="data" format="txt,tabular" label="aligned nanopore events"
20 help="a nanopolish eventalign output that aligns the nanopore events to a reference" /> 26 help="a nanopolish eventalign output that aligns the nanopore events to a reference" />
21 <param name="eventalign_summary" type="data" format="txt,tabular" label="nanopore eventalign summary" 27 <param name="eventalign_summary" type="data" format="txt,tabular" label="nanopore eventalign summary"
22 help="a summary of nanopolish eventalign by read_name,read_index" /> 28 help="a summary of nanopolish eventalign by read_name,read_index" />
23 </inputs> 29 </inputs>
24 30
25 <outputs> 31 <outputs>
26 <data format="txt" name="data_index" label="data.index" from_work_dir="./out/data.index" /> 32 <data format="txt" name="data_index" label="data.index" />
27 <data format="h5" name="eventalign_hdf5" label="eventalign.hdf5" from_work_dir="./out/eventalign.hdf5" /> 33 <data format="h5" name="eventalign_hdf5" label="eventalign.hdf5" />
28 <data format="txt" name="data_log" label="data.log" from_work_dir="./out/data.log" /> 34 <data format="txt" name="data_log" label="data.log" />
29 <data format="txt" name="eventalign_log" label="eventalign.log" from_work_dir="./out/eventalign.log" /> 35 <data format="txt" name="eventalign_log" label="eventalign.log" />
30 <data format="txt" name="data_readcount" label="data.readcount" from_work_dir="./out/data.readcount" /> 36 <data format="txt" name="data_readcount" label="data.readcount" />
31 <data format="json" name="data_json" label="data.json" from_work_dir="./out/data.json"/> 37 <data format="json" name="data_json" label="data.json" />
32 </outputs> 38 </outputs>
33 39
34 <tests> 40 <tests>
35 <test> 41 <test>
36 <param name="eventalign_reads" value="dataprep_eventaligh_reads.tsv" ftype="tabular" /> 42 <param name="eventalign_reads" value="dataprep_eventaligh_reads.tsv" ftype="tabular" />