Mercurial > repos > iuc > rgrnastar

annotate macros.xml @ 28:3e94726bfa9d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
author iuc
date Sun, 11 Feb 2024 00:01:54 +0000
parents 79de45b5069b
children b0f2be869d6d
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1 <macros>
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2 <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@
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3 whenever you make changes to the @TOOL_VERSION@ token!
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4 The data manager uses a symlink to this macro file to keep the STAR and
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5 the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
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6 <!-- STAR version to be used -->
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7 <token name="@TOOL_VERSION@">2.7.11a</token>
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8 <token name="@VERSION_SUFFIX@">0</token>
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9 <token name="@PROFILE@">21.01</token>
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10 <!-- STAR index version compatible with this version of STAR
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11 This is the STAR version that introduced the index structure expected
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12 by the current version.
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13 It can be found for any specific version of STAR with:
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14 STAR -h | grep versionGenome
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15 or by looking for the versionGenome parameter in source/parametersDefault
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16 of STAR's source code -->
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17 <token name="@IDX_VERSION@">2.7.4a</token>
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18 <token name="@IDX_VERSION_SUFFIX@">0</token>
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19 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
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21 <xml name="requirements">
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22 <requirements>
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23 <requirement type="package" version="@TOOL_VERSION@">star</requirement>
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24 <requirement type="package" version="1.18">samtools</requirement>
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25 <requirement type="package" version="1.13">gzip</requirement>
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26 <yield />
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27 </requirements>
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28 </xml>
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30 <xml name="edam">
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31 <edam_topics>
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32 <edam_topic>topic_3170</edam_topic>
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33 <edam_topic>topic_3308</edam_topic>
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34 </edam_topics>
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35 <edam_operations>
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36 <edam_operation>operation_0292</edam_operation>
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37 </edam_operations>
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38 </xml>
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39
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40 <xml name="index_selection" token_with_gene_model="0">
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41 <param argument="--genomeDir" type="select"
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42 label="Select reference genome"
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43 help="If your genome of interest is not listed, contact the Galaxy team">
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44 <options from_data_table="@IDX_DATA_TABLE@">
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45 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
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46 <filter type="static_value" column="5" value="@IDX_VERSION@" />
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47 <filter type="sort_by" column="2" />
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48 <validator type="no_options" message="No indexes are available for the selected input dataset" />
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49 </options>
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50 </param>
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51 </xml>
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52
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53 <token name="@FASTQ_GZ_OPTION@">
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54 --readFilesCommand zcat
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55 </token>
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56 <xml name="citations">
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57 <citations>
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58 <citation type="doi">10.1093/bioinformatics/bts635</citation>
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59 </citations>
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60 </xml>
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61 <xml name="SJDBOPTIONS">
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62 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>
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63 <param argument="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: 'exon', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as 'gene', 'transcript', 'CDS'."/>
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64 <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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65 </xml>
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66 <xml name="dbKeyActions">
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67 <actions>
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68 <expand macro="dbKeyAction"/>
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69 </actions>
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70 </xml>
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71 <xml name="dbKeyAction">
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72 <conditional name="refGenomeSource.geneSource">
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73 <when value="indexed">
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74 <action type="metadata" name="dbkey">
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75 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
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76 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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77 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
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78 </option>
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79 </action>
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80 </when>
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81 <when value="history">
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iuc
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82 <action type="metadata" name="dbkey">
4df95e2d7f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
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83 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
4df95e2d7f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 23
diff changeset
84 </action>
4df95e2d7f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 23
diff changeset
85 </when>
4df95e2d7f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 23
diff changeset
86 </conditional>
4df95e2d7f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
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diff changeset
87 </xml>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
88 <token name="@TEMPINDEX@"><![CDATA[
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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89 ## Create temporary index for custom reference
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
90 #if str($refGenomeSource.geneSource) == 'history':
23
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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91 #if $refGenomeSource.genomeFastaFiles.ext == "fasta"
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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92 ln -s '$refGenomeSource.genomeFastaFiles' refgenome.fa &&
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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diff changeset
93 #else
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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diff changeset
94 gunzip -c '$refGenomeSource.genomeFastaFiles' > refgenome.fa &&
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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95 #end if
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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96 mkdir -p tempstargenomedir &&
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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97 STAR
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
98 --runMode genomeGenerate
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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99 --genomeDir 'tempstargenomedir'
23
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100 --genomeFastaFiles refgenome.fa
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d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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101 ## Handle difference between indices with/without annotations
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iuc
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102 #if 'GTFconditional' in $refGenomeSource:
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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103 ## GTFconditional exists only in STAR, but not STARsolo
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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104 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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105 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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106 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
27
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
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107 --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}'
15
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108 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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diff changeset
109 --sjdbGTFtagExonParentTranscript Parent
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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diff changeset
110 #end if
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 14
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111 #end if
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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diff changeset
112 #else:
27
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diff changeset
113 ## ref genome selection is less complex for STARsolo because
15
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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114 ## with-gtf is mandatory there
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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parents: 14
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115 --sjdbOverhang '${refGenomeSource.sjdbOverhang}'
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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116 --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}'
27
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
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117 --sjdbGTFfeatureExon '${refGenomeSource.sjdbGTFfeatureExon}'
15
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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diff changeset
118 #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3':
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
119 --sjdbGTFtagExonParentTranscript Parent
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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120 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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121 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
122 #if str($refGenomeSource.genomeSAindexNbases):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
123 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
124 #end if
28
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
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diff changeset
125 ## Diploid mode
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iuc
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diff changeset
126 #if 'diploidconditional' in $refGenomeSource:
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
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diff changeset
127 #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
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diff changeset
128 --genomeTransformVCF '${refGenomeSource.diploidconditional.genomeTransformVCF}'
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
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diff changeset
129 --genomeTransformType Diploid
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iuc
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diff changeset
130 #end if
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
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diff changeset
131 #end if
10
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diff changeset
132 --runThreadN \${GALAXY_SLOTS:-4}
23
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iuc
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diff changeset
133 ## in bytes
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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diff changeset
134 --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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135 &&
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 8
diff changeset
136 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
137 ]]></token>
12
39bde80cd248 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
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diff changeset
138 <token name="@REFGENOMEHANDLING@" ><![CDATA[
10
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diff changeset
139 --runThreadN \${GALAXY_SLOTS:-4}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
140 --genomeLoad NoSharedMemory
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
141 --genomeDir
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
142 #if str($refGenomeSource.geneSource) == 'history':
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 8
diff changeset
143 tempstargenomedir
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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144 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
145 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
146 ## Handle difference between indices with/without annotations
23
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iuc
parents: 18
diff changeset
147 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf':
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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diff changeset
148 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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diff changeset
149 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
27
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
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diff changeset
150 --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}'
23
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 18
diff changeset
151 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 18
diff changeset
152 --sjdbGTFtagExonParentTranscript Parent
10
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diff changeset
153 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
154 #end if
23
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iuc
parents: 18
diff changeset
155 #end if
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 18
diff changeset
156 ]]></token>
17
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 16
diff changeset
157 <token name="@READSHANDLING@" ><![CDATA[
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 16
diff changeset
158 ## Check that the input pairs are of the same type
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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diff changeset
159 ## otherwise STARsolo will run for a long time and then error out.
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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diff changeset
160 ## We consume either repeats of two inputs R1 + R2
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 16
diff changeset
161 ## or a collection of paired reads.
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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parents: 16
diff changeset
162 #if str($sc.input_types.use) == "repeat":
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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parents: 16
diff changeset
163 #set $reads1 = []
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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parents: 16
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164 #set $reads2 = []
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165 #for $r1, $r2 in zip($sc.input_types.input1, $sc.input_types.input2):
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166 #assert $r1.datatype == $r2.datatype
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167 #silent $reads1.append(str($r1))
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168 #silent $reads2.append(str($r2))
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169 #end for
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170 #set $reads1 = ','.join($reads1)
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171 #set $reads2 = ','.join($reads2)
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172 #elif str($sc.input_types.use) == "list_paired":
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173 #set $r1 = $sc.input_types.input_collection.forward
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174 #set $r2 = $sc.input_types.input_collection.reverse
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175 #set $reads1 = $r1
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176 #set $reads2 = $r2
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177 #end if
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178 ## cDNA sequence(s) [R2] always go first, then barcode(s) [R1]
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179 ## see: Section 3.2 of STAR manual for multiple inputs, and Section 13 for STARsolo inputs
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180 --readFilesIn $reads2 $reads1
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181 --soloCBmatchWLtype $sc.soloCBmatchWLtype
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182 #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
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183 @FASTQ_GZ_OPTION@
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184 #end if
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185 ]]></token>
23
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186 <token name="@LIMITS@" ><![CDATA[
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187 --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000))
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188 --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000))
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189 --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000))
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190 ]]></token>
15
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191 <xml name="ref_selection">
23
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192 <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome" />
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193 <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/>
15
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194 </xml>
10
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195 <xml name="stdio" >
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196 <stdio>
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197 <regex match="FATAL error" source="both" level="fatal"/>
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198 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
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199 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
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200 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
12
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201 <yield />
10
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202 </stdio>
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203 </xml>
17
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204 <xml name="input_selection">
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205 <conditional name="input_types" >
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206 <param name="use" type="select" label="Input Type" >
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207 <option value="repeat" >Separate barcode and cDNA reads</option>
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208 <option value="list_paired" >Paired collection of barcode and cDNA reads</option>
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209 </param>
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210 <when value="repeat">
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211 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true"
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212 label="RNA-Seq FASTQ/FASTA file, Barcode reads" />
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213 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true"
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214 label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
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215 </when>
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216 <when value="list_paired">
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217 <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs" />
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218 </when>
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219 </conditional>
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220 </xml>
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221 <xml name="input_selection_smart_seq">
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222 <conditional name="input_types_smart_seq" >
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223 <param name="use" type="select" label="Input Type" >
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224 <option value="list_single_end" >Single-end FASTQ collection</option>
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225 <option value="list_paired_end" >Paired FASTQ collection</option>
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226 </param>
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227 <when value="list_single_end">
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228 <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files" />
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229 </when>
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230 <when value="list_paired_end">
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231 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" />
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232 </when>
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233 </conditional>
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234 </xml>
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235 <xml name="umidedup_options">
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236 <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other (1MM_All)</option>
18
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237 <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option>
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238 <option value="1MM_Directional" >Directional with stringent UMI deduplication</option>
17
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239 </xml>
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240 <xml name="anchor_types">
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241 <option value="0">Read start</option>
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242 <option value="1">Read end</option>
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243 <option value="2">Adapter start</option>
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244 <option value="3">Adapter end</option>
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245 </xml>
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246 <xml name="cb_match_wl_common">
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247 <option value="Exact" >Exact</option>
24
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248 <option value="1MM" >Single match (1MM)</option>
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249 </xml>
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250 <xml name="cb_match_wl_cellranger">
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251 <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2, 1MM_multi)</option>
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252 <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3, 1MM_multi_pseudocounts)</option>
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253 <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3, 1MM_multi_Nbase_pseudocounts)</option>
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254 </xml>
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255 <xml name="solo_adapter_params">
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256 <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." >
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257 <sanitizer>
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258 <valid initial="string.digits">
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259 <add value="-"/>
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260 <add value="A"/>
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261 <add value="T"/>
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262 <add value="C"/>
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263 <add value="G"/>
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264 <add value="N"/>
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265 </valid>
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266 </sanitizer>
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267 </param>
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268 <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence" />
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269 <param argument="--clipAdapterType" type="select" >
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270 <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option>
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271 <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option>
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272 <option value="None" >No adapter clipping</option>
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273 </param>
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274 </xml>
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275 <xml name="common_SAM_attributes">
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276 <option value="NH" selected="true">NH (number of reported alignments/hits for the read)</option>
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277 <option value="HI" selected="true">HI (query hit index)</option>
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278 <option value="AS" selected="true">AS (local alignment score)</option>
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279 <option value="nM" selected="true">nM (number of mismatches per (paired) alignment)</option>
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280 <option value="NM">NM (edit distance of the aligned read to the reference)</option>
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281 <option value="MD">MD (string for mismatching positions)</option>
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282 <option value="jM">jM (intron motifs for all junctions)</option>
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283 <option value="jI">jI (1-based start and end of introns for all junctions)</option>
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284 </xml>
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285 <xml name="limits">
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286 <section name="junction_limits" title="Junction Limits" expanded="false">
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287 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
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288 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
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289 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
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290 </section>
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291 </xml>
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292 <xml name="outCountActions">
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293 <actions>
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294 <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
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295 <expand macro="dbKeyAction"/>
23
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296 </actions>
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297 </xml>
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298 <xml name="outWig">
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299 <conditional name="outWig">
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300 <param name="outWigType" type="select" label="Compute coverage">
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301 <option value="None">No coverage</option>
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302 <option value="bedGraph">Yes in bedgraph format</option>
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303 <option value="wiggle">Yes in wiggle format</option>
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304 </param>
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305 <when value="None">
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306 <!-- This is necessary for the filtering of output -->
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307 <param name="outWigStrand" type="hidden" value="false" />
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308 </when>
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309 <when value="bedGraph">
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310 <expand macro="outWigParams"/>
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311 </when>
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312 <when value="wiggle">
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313 <expand macro="outWigParams"/>
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314 </when>
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315 </conditional>
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316 </xml>
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317 <xml name="outWigParams">
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318 <param name="outWigTypeSecondWord" type="select" label="Input for coverage">
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319 <option value="">Default (everything that mapped)</option>
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320 <option value="read_5p">signal from only 5’ of the 1st read</option>
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321 <option value="read2">signal from only 2nd read</option>
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322 </param>
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323 <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="Generate a coverage for each strand (stranded coverage)"/>
23
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324 <param argument="--outWigReferencesPrefix" type="text" value="-" label="prefix matching reference name" help="For example, set 'chr' if you mapped on an ensembl genome but you want to display on UCSC"/>
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325 <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/>
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326 </xml>
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327 <token name="@OUTWIG@"><![CDATA[
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328 #if str($outWig.outWigType) != 'None':
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329 --outWigType '$outWig.outWigType' '$outWig.outWigTypeSecondWord'
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330 --outWigStrand '$outWig.outWigStrand'
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331 --outWigReferencesPrefix '$outWig.outWigReferencesPrefix'
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332 --outWigNorm '$outWig.outWigNorm'
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333 #end if
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334 ]]></token>
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335 <token name="@OUTWIGOUTPUTS@"><![CDATA[
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336 #if str($outWig.outWigType) == "bedGraph":
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337 && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out
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338 && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out
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339 #if str($outWig.outWigStrand) == "Stranded":
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340 && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out
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341 && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out
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342 #end if
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343 #elif str($outWig.outWigType) == "wiggle":
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344 && mv Signal.Unique.str1.out.wig Signal.Unique.str1.out
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345 && mv Signal.UniqueMultiple.str1.out.wig Signal.UniqueMultiple.str1.out
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346 #if str($outWig.outWigStrand) == "Stranded":
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347 && mv Signal.Unique.str2.out.wig Signal.Unique.str2.out
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348 && mv Signal.UniqueMultiple.str2.out.wig Signal.UniqueMultiple.str2.out
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349 #end if
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350 #end if
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351 ]]></token>
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352 <xml name="outWigOutputs">
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353 <data format="bedgraph" name="signal_unique_str1" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 1" from_work_dir="Signal.Unique.str1.out">
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354 <filter>outWig['outWigType'] != "None"</filter>
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355 <expand macro="dbKeyActions" />
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356 <change_format>
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357 <when input="outWig.outWigType" value="wiggle" format="wig" />
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358 </change_format>
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359 </data>
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360 <data format="bedgraph" name="signal_uniquemultiple_str1" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 1" from_work_dir="Signal.UniqueMultiple.str1.out">
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361 <filter>outWig['outWigType'] != "None"</filter>
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362 <expand macro="dbKeyActions" />
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363 <change_format>
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364 <when input="outWig.outWigType" value="wiggle" format="wig" />
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365 </change_format>
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366 </data>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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367 <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out">
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368 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
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369 <expand macro="dbKeyActions" />
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370 <change_format>
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371 <when input="outWig.outWigType" value="wiggle" format="wig" />
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372 </change_format>
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373 </data>
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374 <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out">
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375 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
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376 <expand macro="dbKeyActions" />
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377 <change_format>
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378 <when input="outWig.outWigType" value="wiggle" format="wig" />
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379 </change_format>
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380 </data>
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381 </xml>
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382 <xml name="quantMode">
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383 <conditional name="quantmode_output">
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384 <param argument="--quantMode" type="select"
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385 label="Per gene/transcript output"
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386 help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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387 <option value="-">No per gene or transcript output</option>
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388 <option value="GeneCounts">Per gene read counts (GeneCounts)</option>
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389 <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>
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390 <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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391 </param>
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392 <when value="-" />
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393 <when value="GeneCounts" />
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394 <when value="TranscriptomeSAM">
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395 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
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396 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
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397 help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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398 </when>
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399 <when value="TranscriptomeSAM GeneCounts">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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400 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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401 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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402 help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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403 </when>
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404 </conditional>
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405 </xml>
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406 <xml name="quantModeNoGTF">
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407 <conditional name="quantmode_output">
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408 <param argument="--quantMode" type="select"
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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409 label="Per gene/transcript output">
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410 <option value="-">No per gene or transcript output as no GTF was provided</option>
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411 </param>
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412 <when value="-" />
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413 </conditional>
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414 </xml>
24
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415 <xml name="outSAMmapqUnique">
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416 <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value
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417 - according to SAM/BAM specs it means "undefined".
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418 - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. -->
4df95e2d7f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
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419 <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255"
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420 label="MAPQ value for unique mappers"
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421 help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is
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422 used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." />
4df95e2d7f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
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423 </xml>
3
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424 </macros>