Mercurial > repos > earlhaminst > gstf_preparation

annotate gstf_preparation.xml @ 0:28879ca33b5f draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
author earlhaminst
date Wed, 15 Mar 2017 20:18:57 -0400
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28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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1 <tool id="gstf_preparation" name="GeneSeqToFamily preparation" version="0.3.0">
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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2 <description>converts data for the workflow</description>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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3 <command detect_errors="exit_code">
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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4 <![CDATA[
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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5 python '$__tool_directory__/gstf_preparation.py'
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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6 #for $q in $queries
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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7 --gff3 '${q.genome}:${q.gff3_input}'
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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8 #end for
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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9 #if str($json) != 'None'
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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10 #for $v in $json
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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11 --json '$v'
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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12 #end for
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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13 #end if
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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14 #for $fasta_input in $fasta_inputs
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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15 --fasta '${fasta_input}'
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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16 #end for
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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17 -o '$output_db'
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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18 --of '$output_fasta'
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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19 ]]>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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20 </command>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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21
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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22 <inputs>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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23 <repeat name="queries" title="GFF3 dataset">
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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24 <param name="gff3_input" type="data" format="gff3" label="GFF3 dataset" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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25 <param name="genome" type="text" label="Genome name" help="Genome name without whitespaces or special characters">
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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26 <validator type="empty_field" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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27 </param>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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28 </repeat>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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29 <param name="json" type="data" format="json" multiple="true" optional="true" label="Gene features in JSON format generated by 'Get features by Ensembl ID' tool" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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30 <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding FASTA datasets" help="Each FASTA header line should start with a transcript id" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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31 </inputs>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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32
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33 <outputs>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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34 <data name="output_db" format="sqlite" label="${tool.name} on ${on_string}: SQLite" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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35 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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36 </outputs>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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37
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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38 <tests>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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39 <test>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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40 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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41 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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42 <param name="genome" value="caenorhabditis_elegans" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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43 <output name="output_db" file="test1.sqlite" compare="sim_size" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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44 <output name="output_fasta" file="test1.fasta" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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45 </test>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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46 <test>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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47 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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48 <param name="json" ftype="json" value="gene.json" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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49
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50 <output name="output_db" file="test2.sqlite" compare="sim_size" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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51 <output name="output_fasta" file="test2.fasta" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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52 </test>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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53 </tests>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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54 <help>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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55 <![CDATA[
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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56 **What it does**
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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57
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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58 This tool converts a set of GFF3 and/or JSON gene feature information datasets into SQLite format and modify the header lines of a corresponding CDS FASTA to be used with the GeneSeqToFamily workflow.
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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59
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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60 Example GFF3 file::
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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61
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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62 scaffold_0 MYZPE13164_Clone_G006_v1.0 gene 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030;biotype=protein_coding
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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63 scaffold_0 MYZPE13164_Clone_G006_v1.0 mRNA 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1;Parent=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030.1;biotype=protein_coding;_AED=0.31
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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64 scaffold_0 MYZPE13164_Clone_G006_v1.0 three_prime_utr 44968 46637 . - . ID=MYZPE13164_G006_v1.0_000000030.1.3utr1;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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65 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 44968 47432 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon1;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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66 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 46638 47432 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds1;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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67 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 53325 53539 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon2;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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68 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 53325 53539 . - 2 ID=MYZPE13164_G006_v1.0_000000030.1.cds2;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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69 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 54614 54719 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon3;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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70 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 54614 54719 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds3;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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71 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 54852 55106 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds4;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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72 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 54852 55117 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon4;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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73 scaffold_0 MYZPE13164_Clone_G006_v1.0 five_prime_utr 55107 55117 . - . ID=MYZPE13164_G006_v1.0_000000030.1.5utr1;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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74 scaffold_0 MYZPE13164_Clone_G006_v1.0 five_prime_utr 68851 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1.5utr2;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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75 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 68851 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon5;Parent=MYZPE13164_G006_v1.0_000000030.1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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76
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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77 The following features are parsed: **gene**, **mRNA**, **transcript**, **exon**, **five_prime_utr**, **three_prime_utr** and **CDS**, all other are ignored. Also, **ID** and **Parent** tags are needed to create relations.
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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78 ]]>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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79 </help>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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80 <citations>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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81 </citations>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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82 </tool>