Mercurial > repos > jpayne > snp_pipeline

comparison 0_index_ref.xml.old @ 0:eefdd97a6749

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit b'7f6183b769772449fbcee903686b8d5ec5b7439f\n'-dirty
author jpayne
date Wed, 24 Jan 2018 14:18:21 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:eefdd97a6749
1 <tool id="index_ref" name="0. Get or Build Index" version="1.0.1" profile="16.10">
2 <description>by lookup from BioProject or from an assembly</description>
3 <requirements>
4 <requirement type="package" version="2.3.4">bowtie2</requirement>
5 <requirement type="package" version="1.6">samtools</requirement>
6 <requirement type="package" version="1.5.11">boto3</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 #if $source.source_select == 'bioproject'
10 ${__tool_directory__}/snp-cache.py snp_bioproject_references "${bioproject}" -o ${output} &&
11 ${__tool_directory__}/snp-cache.py snp_bioproject_indexes "${bioproject}" -o ${faidx}
12 #else
13 mkdir ./reference &&
14 cp ${input} ./reference/reference.fasta &&
15 export ID=\$(md5sum $input | cut -c -32) &&
16 ${__tool_directory__}/snp-cache.py snp_local_references \$ID
17 -c "
18 bowtie2-build ./reference/reference.fasta --quiet --threads \${GALAXY_SLOTS:-4} ./reference/reference &&
19 tar -zcf /dev/stdout ./reference/ref*bt2
20 "
21 -o ${output}
22 -l $cache_log
23
24 ##&& ${__tool_directory__}/snp-cache.py snp_local_indexes \$ID
25 ## -c "
26 ## samtools faidx ./reference/reference.fasta && cat ./reference/reference.fasta.fai
27 ## "
28 ## -o ${faidx}
29 #end if
30 && cat $cache_log
31 ]]></command>
32 <inputs>
33 <conditional name="source">
34 <param name="source_select" type="select" label="Use the reference associated with a provided BioProject, a curated GalaxyTrakr reference, or a reference from your history">
35 <option value="bioproject">Provide a BioProject</option>
36 <option value="curated">Use a GalaxyTrakr reference</option>
37 <option value="history">Use a reference from your history</option>
38 </param>
39 <when value="bioproject">
40 <param type="data" name="bioproject" format="text"/>
41 </when>
42 <when value="curated">
43 <param name="input" type="select" label="Select reference fasta">
44 <options from_data_table="all_fasta">
45 <filter type="sort_by" column="2"/>
46 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
47 </options>
48 </param>
49 </when>
50 <when value="history">
51 <param type="data" name="input" format="fasta" label="Select reference FASTA"/>
52 </when>
53 </conditional>
54 </inputs>
55 <outputs>
56 <data label="Indexed reference (bt2)" name="output" format="tar" />
57 <!-- <data label="Indexed reference (faidx)" name="faidx" format="fai" /> -->
58 <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
59 </outputs>
60 <tests>
61 <test>
62 <param name="source_select" value="history" />
63 <param name="input" value="reference/lambda_virus.fasta" />
64 <output name="output" value="reference/reference.tar.gz" decompress="true" lines_diff="10" />
65 <!-- <output name="faidx" value="reference/reference.fasta.fai" /> -->
66 </test>
67 </tests>
68 <help><![CDATA[
69 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
70 ]]></help>
71 <citations>
72 <citation type="doi">10.7717/peerj-cs.20</citation>
73 <!-- <citation type="bibtex">
74 @misc{cfsan-snp-pipeline,
75 author = {Steve Davis and James Pettengill and Yan Luo and Justin Payne and Albert Shpuntoff and Rugh Rand and Errol Strain},
76 year = {2015},
77 title = {CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data},
78 url = {https://doi.org/10.7717/peerj-cs.20},
79 journal = {PeerJ Computer Science},
80 }</citation> -->
81 </citations>
82 </tool>