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annotate spaln.xml @ 0:95ea8d97abb4 draft

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planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
author iuc
date Fri, 11 Jan 2019 18:15:21 -0500
parents
children 37b5e1f0b544
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95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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1 <tool id="spaln" name="Spaln: align cDNA or Protein to genome" version="@TOOL_VERSION@+galaxy0">
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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2 <description>Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.3.2</token>
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5 </macros>
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6 <edam_topics>
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7 <edam_topic>topic_3512</edam_topic>
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8 </edam_topics>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">spaln</requirement>
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11 </requirements>
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12 <command detect_errors="aggressive"><![CDATA[
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13 spaln -t\${GALAXY_SLOTS:-1} -O$format -o '$output1' '$genome' '$query'
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14 ]]></command>
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15 <inputs>
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16 <param type="data" name="genome" format="fasta" label="Genome sequence to search (FASTA format)" />
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17 <param type="data" name="query" format="fasta" label="Query sequence(s) (protein or cDNA)" />
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18 <param argument="-O" type="select" name="format" label="Output format">
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19 <option value="0">GFF3 format genes</option>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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20 <option value="2">GFF3 format matches</option>
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21 <option value="3">BED format</option>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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22 <option value="4">Tabular format exon information</option>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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23 </param>
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24 </inputs>
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25 <outputs>
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26 <data name="output1" format="tabular">
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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27 <change_format>
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28 <!-- these values correspond with the format options of the spaln command, not all of which are current supported -->
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29 <when input="format" value="0" format="gff3" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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30 <when input="format" value="2" format="gff3" />
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31 <when input="format" value="3" format="bed12" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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32 <when input="format" value="4" format="tabular" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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33 </change_format>
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34 <!-- <actions> .. <conditional> .. <when> .. <action> current does not work in Galaxy,
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35 something that https://github.com/galaxyproject/galaxy/pull/7197 is addressing, so this is
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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36 commented out till that is merged
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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37 <actions>
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38 <conditional name="format">
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39 <when value="4">
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40 <action type="metadata" name="column_names" default="rID,gID,%id,ExonL,MisMch,Unpair,ref_l,ref_r,tgt_l,tgt_r,eScore,IntrnL,iScore,Sig3/I,Sig5/T # - X P DiNuc" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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41 </when>
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42 </conditional>
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43 </actions>
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44 -->
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45 </data>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="genome" ftype="fasta" value="genome.fasta" />
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50 <param name="query" ftype="fasta" value="query.fasta" />
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51 <param name="format" value="0"/>
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52 <output name="output1" value="output1_gff_genes.gff3" />
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53 </test>
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54 <test>
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55 <param name="genome" ftype="fasta" value="genome.fasta" />
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56 <param name="query" ftype="fasta" value="query.fasta" />
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57 <param name="format" value="2"/>
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58 <output name="output1" value="output1_gff_matches.gff3" />
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59 </test>
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60 <test>
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61 <param name="genome" ftype="fasta" value="genome.fasta" />
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62 <param name="query" ftype="fasta" value="query.fasta" />
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63 <param name="format" value="3"/>
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64 <output name="output1" value="output1.bed12" />
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65 </test>
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66 <test>
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67 <param name="genome" ftype="fasta" value="genome.fasta" />
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68 <param name="query" ftype="fasta" value="query.fasta" />
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69 <param name="format" value="4"/>
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70 <output name="output1" value="output1.tabular" />
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74 Spaln_ (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or
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75 protein sequences onto a whole genomic sequence in a single job.
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76
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77 This Galaxy wrapper currently only supports the default (i.e. *-O3*) algorithm for Spaln with default parameters.
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78
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79 .. _Spaln: http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/
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80 ]]></help>
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81 <citations>
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82 <citation type="doi">0.1093/nar/gkn105</citation>
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83 </citations>
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84 </tool>