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comparison pangolin.xml @ 1:b91b3923656e draft

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"planemo upload for repository https://github.com/hCoV-2019/pangolin commit 216d09e3d63a6ab4245df78c111ca97d4e0b14de"
author nml
date Fri, 01 May 2020 15:33:17 -0400
parents f612c8391bd8
children c897e502c084
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0:f612c8391bd8 1:b91b3923656e
1 <tool id="pangolon" name="Pangolin" version="@VERSION@+galaxy0"> 1 <tool id="pangolin" name="Pangolin" version="@VERSION@+galaxy0">
2 <description> CoV-2019 Phylogenetic Assignment of Named Global Outbreak LINeages</description> 2 <description> CoV-2019 Phylogenetic Assignment of Named Global Outbreak LINeages</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 8
9 pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' 9 pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' &&
10 10
11 sed 's/,/\t/g' lineage_report.csv > lineage_report.tsv
11 ]]></command> 12 ]]></command>
12 <inputs> 13 <inputs>
13 <param name="input1" type="data" format="fasta" 14 <param name="input1" type="data" format="fasta"
14 label="Input multi-sequence fasta file" 15 label="Input multi-sequence fasta file"
15 /> 16 />
23 argument="--min-length" 24 argument="--min-length"
24 /> 25 />
25 </section> 26 </section>
26 </inputs> 27 </inputs>
27 <outputs> 28 <outputs>
28 <data format="csv" from_work_dir="lineage_report.csv" name="lineage_report" label="${input1.name}_lineage_report" /> 29 <data format="tabular" from_work_dir="lineage_report.tsv" name="lineage_report" label="${input1.name}_lineage_report" />
29 </outputs> 30 </outputs>
30 <tests> 31 <tests>
31 <test> 32 <test>
32 <param name="input1" value="test_seqs.fasta" /> 33 <param name="input1" value="test_seqs.fasta" />
33 <output name="lineage_report" value="lineage_report.csv" /> 34 <output name="lineage_report" value="lineage_report.tsv" />
34 </test> 35 </test>
35 </tests> 36 </tests>
36 <help><![CDATA[ 37 <help><![CDATA[
37 38
38 Pangolin 39 Pangolin