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