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annotate ensembl_longest_cds_per_gene.xml @ 2:6cf9f7f6509c draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 651fae48371f845578753052c6fe173e3bb35670
author earlhaminst
date Wed, 15 Mar 2017 20:23:13 -0400
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6cf9f7f6509c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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1 <tool id="ensembl_longest_cds_per_gene" name="Select longest CDS per gene" version="0.0.2">
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4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
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2 <description>from Ensembl CDS FASTA</description>
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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3 <command detect_errors="exit_code"><![CDATA[
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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4 python '$__tool_directory__/ensembl_longest_cds_per_gene.py' -f '$input' -o '$output'
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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5 ]]></command>
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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6 <inputs>
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7 <param name="input" type="data" format="fasta" label="CDS FASTA from Ensembl" />
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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8 </inputs>
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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9 <outputs>
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earlhaminst
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10 <data name="output" format="fasta" label="${tool.name} on ${on_string}" />
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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11 </outputs>
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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12 <tests>
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earlhaminst
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13 <test>
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earlhaminst
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14 <param name="input" ftype="fasta" value="Mus_musculus.GRCm38.cds.first100.fa" />
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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15 <output name="output" file="Mus_musculus.GRCm38.cds.longest.fa" />
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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16 </test>
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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17 </tests>
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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18 <help><![CDATA[
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a07680f3033a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit c1b5d458dcd1256516916ac5476e02a0ff3398de
earlhaminst
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19 This tool filters a CDS FASTA file from Ensembl retaining only the longest CDS sequence for each gene.
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4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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21 The headers of the input CDS FASTA file are expected to be of the following format::
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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23 >ENSMUST00000177965.1 cds chromosome:GRCm38:12:113456720:113456736:-1 gene:ENSMUSG00000094057.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd2-7 description:immunoglobulin heavy diversity 2-7 [Source:MGI Symbol;Acc:MGI:4439866]
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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24
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earlhaminst
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25 Among the CDS sequences having the same gene identifier (ENSMUSG00000094057 in the example above), the tool will select the one with the longest sequence.
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4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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26 ]]></help>
4dba69135845 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 26c70aecb56c19099455bb5a432615b09ad322d1
earlhaminst
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27 </tool>