Mercurial > repos > wolma > rnastar_index_builder

annotate data_manager/macros.xml @ 1:6127cd38980b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
author wolma
date Mon, 24 Jun 2019 11:36:07 -0400
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children 039890bdcb62
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6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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1 <macros>
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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2 <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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3 whenever you make changes to the following two version tokens!
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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4 The data manager uses a symlink to this macro file to keep the versions in
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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5 sync. -->
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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6 <!-- STAR version to be used -->
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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7 <token name="@VERSION@">2.7.1a</token>
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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8 <!-- STAR index version compatible with this version of STAR
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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9 This is the STAR version that introduced the index structure expected
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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10 by the current version.
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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11 It can be found for any specific version of STAR with:
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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12 STAR -h | grep versionGenome
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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13 or by looking for the versionGenome parameter in source/parametersDefault
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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14 of STAR's source code -->
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15 <token name="@IDX_VERSION@">2.7.1a</token>
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17 <xml name="requirements">
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18 <requirements>
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19 <requirement type="package" version="@VERSION@">star</requirement>
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20 <requirement type="package" version="1.9">samtools</requirement>
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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21 </requirements>
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22 </xml>
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24 <xml name="index_selection" token_with_gene_model="1">
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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25 <param argument="--genomeDir" name="genomeDir" type="select"
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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26 label="Select reference genome"
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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27 help="If your genome of interest is not listed, contact the Galaxy team">
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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28 <options from_data_table="rnastar_index2_versioned">
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29 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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30 <filter type="static_value" column="5" value="@IDX_VERSION@" />
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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31 <filter type="sort_by" column="2" />
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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32 <validator type="no_options" message="No indexes are available for the selected input dataset" />
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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33 </options>
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34 </param>
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35 </xml>
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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36
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37 <token name="@FASTQ_GZ_OPTION@">
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38 --readFilesCommand zcat
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39 </token>
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40 <xml name="citations">
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41 <citations>
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42 <citation type="doi">10.1093/bioinformatics/bts635</citation>
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43 </citations>
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44 </xml>
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45 <xml name="@SJDBOPTIONS@" token_optional="true">
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46 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/>
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47 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
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48 </xml>
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49 <xml name="dbKeyActions">
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50 <actions>
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51 <conditional name="refGenomeSource.geneSource">
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52 <when value="indexed">
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53 <action type="metadata" name="dbkey">
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54 <option type="from_data_table" name="rnastar_index2_versioned" column="1" offset="0">
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55 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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56 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
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57 </option>
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58 </action>
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59 </when>
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60 <when value="history">
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61 <action type="metadata" name="dbkey">
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62 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
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63 </action>
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64 </when>
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65 </conditional>
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66 </actions>
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67 </xml>
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68 </macros>