annotate rg_rnaStarSolo.xml @ 14:1cd2511a396e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
author iuc
date Wed, 22 Feb 2023 18:01:29 +0000
parents 9ee34ba73ebf
children b8f5f6e87f5c
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1 <tool id="rna_starsolo" name="RNA STARSolo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>mapping, demultiplexing and gene quantification for single cell RNA-seq</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edam"/>
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7 <xrefs>
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8 <xref type="bio.tools">star</xref>
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9 </xrefs>
0
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10 <expand macro="requirements"/>
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11 <expand macro="stdio" >
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12 <regex match="Segmentation fault" source="both" level="fatal" />
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13 </expand>
0
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e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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15 <command><![CDATA[
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16 @TEMPINDEX@
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17 STAR
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18 @REFGENOMEHANDLING@
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19
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20 ## Supports Drop-seq, 10X Chromium, inDrop and Smart-Seq
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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21 --soloType $sc.solo_type
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23 #if str($sc.solo_type) == "CB_UMI_Simple":
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24 @READSHANDLING@
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25 #if $sc.soloCBwhitelist:
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26 --soloCBwhitelist '$sc.soloCBwhitelist'
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27 #else
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28 --soloCBwhitelist None
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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29 #end if
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30 ## 1 - check length of barcode, 0 - do not check
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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31 ## Good for checking custom chemistries
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32 --soloBarcodeReadLength $sc.soloBarcodeReadLength
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33 #if str($sc.params.chemistry) == "Cv2":
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34 --soloCBstart 1
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35 --soloCBlen 16
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36 --soloUMIstart 17
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37 --soloUMIlen 10
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38 #else if str($sc.params.chemistry) == "Cv3":
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39 --soloCBstart 1
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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40 --soloCBlen 16
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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41 --soloUMIstart 17
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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42 --soloUMIlen 12
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43 #else if str($sc.params.chemistry) == "custom":
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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44 --soloCBstart $sc.params.soloCBstart
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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45 --soloCBlen $sc.params.soloCBlen
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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46 --soloUMIstart $sc.params.soloUMIstart
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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47 --soloUMIlen $sc.params.soloUMIlen
10
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48 #if $sc.params.bccdna_mate.bc_location == "same_mate":
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49 --soloBarcodeMate $sc.params.bccdna_mate.soloBarcodeMate
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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50 #if $sc.params.bccdna_mate.soloBarcodeMate == "1":
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51 --clip5pNbases $sc.params.bccdna_mate.clip_n_bases 0
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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52 #else if $sc.params.bccdna_mate.soloBarcodeMate == "2":
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53 --clip3pNbases 0 $sc.params.bccdna_mate.clip_n_bases
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54 #end if
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55 #end if
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56 --soloAdapterSequence '$sc.params.soloAdapterSequence'
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57 --soloAdapterMismatchesNmax $sc.params.soloAdapterMismatchesNmax
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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58 --clipAdapterType $sc.params.clipAdapterType
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59 #end if
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60
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61 #elif str($sc.solo_type) == "CB_UMI_Complex":
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62 @READSHANDLING@
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63 ## inDrop supports multiple cell barcodes of varying length
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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64 #set $cb_whitelist = []
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65 #set $cb_pos = []
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66 #for $cb in $sc.cb_whitelists:
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67 #silent $cb_whitelist.append(str($cb.whitelist_file))
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68 #silent $cb_pos.append('_'.join([str($cb.cb_start_anchor), str($cb.cb_start_anchor_pos),str($cb.cb_end_anchor), str($cb.cb_end_anchor_pos)]))
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69 #end for
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70 #set $cb_whitelist = ' '.join($cb_whitelist)
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71 --soloCBwhitelist $cb_whitelist
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72 #set $cb_pos = ' '.join($cb_pos)
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73 --soloCBposition $cb_pos
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74 #set $umi_pos = '_'.join([str($sc.umi_start_anchor), str($sc.umi_start_anchor_pos), str($sc.umi_end_anchor), str($sc.umi_end_anchor_pos)])
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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75 --soloUMIposition $umi_pos
10
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76 --soloAdapterSequence '$sc.soloAdapterSequence'
9
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77 --soloAdapterMismatchesNmax $sc.soloAdapterMismatchesNmax
10
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78 --clipAdapterType $sc.clipAdapterType
9
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79
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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80 #elif str($sc.solo_type) == "SmartSeq":
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81 ## Create a manifest file with fastq files and their corresponding cell-ids
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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82 ## For Smart-Seq [R1] is followed by [R2]
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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83 --readFilesManifest '$manifest_file'
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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84 #set $read_files_command = ""
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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85 #if str($sc.input_types_smart_seq.use) == "list_single_end":
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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86 #if $sc.input_types_smart_seq.single_end_collection[0].is_of_type('fastq.gz', 'fastqsanger.gz'):
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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87 @FASTQ_GZ_OPTION@
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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88 #end if
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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89 #elif str($sc.input_types_smart_seq.use) == "list_paired_end":
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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90 #if $sc.input_types_smart_seq.paired_end_collection[0].forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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91 @FASTQ_GZ_OPTION@
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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92 #end if
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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93 #end if
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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94 --soloCBwhitelist None
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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95 #end if
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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96
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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97 --soloStrand $solo.soloStrand
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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98 --soloFeatures $solo.soloFeatures
13
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99 --soloUMIdedup $sc.umidedup.soloUMIdedup
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100 #if str($sc.umidedup.soloUMIdedup) == "1MM_CR":
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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101 --soloUMIfiltering $sc.umidedup.soloUMIfiltering
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102 #end if
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103 --quantMode TranscriptomeSAM $solo.quantModeGene
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104 #set $tag_names = str($solo.outSAMattributes).replace(',', ' ')
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105 --outSAMattributes $tag_names
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106 #if "CB" in $tag_names or "UB" in $tag_names or str($outWig.outWigType) != 'None':
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107 --outSAMtype BAM SortedByCoordinate
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108 #else:
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109 --outSAMtype BAM Unsorted
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110 #end if
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111
9
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112 #if str($solo.filter.filter_type) == "cellranger2":
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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113 --soloCellFilter CellRanger2.2 $solo.filter.n_expected $solo.filter.max_perc $solo.filter.max_min_ratio
10
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114 #else if str($solo.filter.filter_type) == "emptydrops":
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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115 --soloCellFilter EmptyDrops_CR $solo.filter.nExpectedCells $solo.filter.maxPercentile $solo.filter.maxMinRatio $solo.filter.indMin $solo.filter.indMax $solo.filter.umiMin $solo.filter.umiMinFracMedian $solo.filter.candMaxN $solo.filter.FDR $solo.filter.simN
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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116 #else if str($solo.filter.filter_type) == "topcells":
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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117 --soloCellFilter TopCells $solo.filter.n_cells
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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118 #else if str($solo.filter.filter_type) == "no_filter":
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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119 --soloCellFilter None
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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120 #end if
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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121 ## Splice junctions are always under "raw" directory
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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122
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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123 --soloOutFormatFeaturesGeneField3 '${solo.soloOutFormatFeaturesGeneField3}'
13
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124
14
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125 ## Unmapped
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126 '$solo.outSAMunmapped'
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127 ## Read MAPQ
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128 --outSAMmapqUnique ${solo.outSAMmapqUnique}
13
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129 ## Limits
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130 @LIMITS@
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131
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132 ##outWig:
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133 @OUTWIG@
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ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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134 ## Rename the the selected features directory
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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135 && mv Solo.out/${solo.soloFeatures} Solo.out/soloFeatures
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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136 ## put the barcodes and features stats into a single file
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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137 && cat <(echo "Barcodes:") Solo.out/Barcodes.stats <(echo "Genes:") Solo.out/soloFeatures/Features.stats > '${output_stats}'
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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138
13
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139
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140 #if "CB" in $tag_names or "UB" in $tag_names or str($outWig.outWigType) != 'None':
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141 ## recompress BAM output for smaller file size
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142 && samtools view -b -o '$output_BAM' Aligned.sortedByCoord.out.bam
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143 #else:
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144 ## BAM sorting (logic copied from samtools_sort wrapper)
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145 ## choosing BAM SortedByCoord appeared once to give fewer reads
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146 ## than BAM Unsorted followed by a samtools sort
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147 ## so better go with the latter?
7
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148
13
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149 &&
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150 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
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151 addthreads=\${GALAXY_SLOTS:-2} && (( addthreads-- )) &&
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152 ##compute the number of memory available to samtools sort (-m)
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153 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
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154 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
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155 ((addmemory=addmemory*75/100)) &&
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156 samtools sort -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}" -O bam -o '$output_BAM' Aligned.out.bam
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157 #end if
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158 ##outWig:
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159 @OUTWIGOUTPUTS@
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160
0
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161 ]]></command>
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162 <configfiles>
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163 <configfile name="manifest_file" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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164 #if str($sc.solo_type) == "SmartSeq":
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165 #set $cellids_fh = open(str($sc.cell_ids), 'r')
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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166 #set $cellids = [str(x.strip()) for x in $cellids_fh.readlines()]
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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167 #silent $cellids_fh.close()
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168 #set $samples = []
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169 #if str($sc.input_types_smart_seq.use) == "list_single_end":
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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170 #assert len($cellids) == len($sc.input_types_smart_seq.single_end_collection.keys())
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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171 #for $i,$r1 in enumerate($sc.input_types_smart_seq.single_end_collection):
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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172 #silent $samples.append('\t'.join([str($r1), '-', 'ID:' + $cellids[$i]]))
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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173 #end for
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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174 #elif str($sc.input_types_smart_seq.use) == "list_paired_end":
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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175 #assert len($cellids) == len($sc.input_types_smart_seq.paired_end_collection.keys())
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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176 #for $i,($r1,$r2) in enumerate($sc.input_types_smart_seq.paired_end_collection):
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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177 #silent $samples.append('\t'.join([str($r1), str($r2), 'ID:' + $cellids[$i]]))
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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178 #end for
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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179 #end if
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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180 #echo '\n'.join($samples)
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181 #end if
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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182 </configfile>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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183 </configfiles>
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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184 <inputs>
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185 <!-- Genome source. -->
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186 <conditional name="refGenomeSource">
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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187 <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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188 <option value="indexed" selected="true">Use a built-in index</option>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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189 <option value="history">Use reference genome from history and create temporary index</option>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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190 </param>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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191 <when value="indexed">
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192 <conditional name="GTFconditional">
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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193 <param name="GTFselect" type="select"
12
79b885ce78d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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194 label="Reference genome with annotation"
7
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195 help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions, and provide your own splice junction annonations.">
14
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
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196 <option value="without-gtf-with-gtf" selected='true'>use genome reference without builtin gene-model</option>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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197 <option value="with-gtf">use genome reference with builtin gene-model</option>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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198 </param>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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199 <when value="with-gtf">
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200 <expand macro="index_selection" with_gene_model="1" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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201 </when>
14
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
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202 <when value="without-gtf-with-gtf">
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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203 <expand macro="index_selection" with_gene_model="0" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 12
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204 <expand macro="SJDBOPTIONS"/>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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205 </when>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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206 </conditional>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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207 </when>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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parents: 5
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208 <when value="history">
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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parents: 5
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209 <expand macro="ref_selection" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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210 <expand macro="SJDBOPTIONS"/>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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211 </when>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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212 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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213 <conditional name="sc" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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214 <param name="solo_type" type="select" label="Type of single-cell RNA-seq" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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215 <option value="CB_UMI_Simple">Drop-seq or 10X Chromium</option>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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216 <option value="CB_UMI_Complex">inDrop</option>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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217 <option value="SmartSeq">Smart-Seq</option>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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218 </param>
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219 <when value="CB_UMI_Simple">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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220 <expand macro="input_selection" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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221 <param format="txt,tsv" argument="--soloCBwhitelist" optional="True" type="data" label="RNA-Seq Cell Barcode Whitelist"/>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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222 <conditional name="params" >
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223 <param name="chemistry" type="select" label="Configure Chemistry Options">
13
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224 <option value="Cv2" selected="true">Chromium chemistry v2</option>
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225 <option value="Cv3">Chromium chemistry v3</option>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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226 <option value="custom">Custom</option>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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227 </param>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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228 <when value="Cv2" />
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229 <when value="Cv3" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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230 <when value="custom" >
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231 <param argument="--soloCBstart" type="integer" min="1" value="1" label="Cell Barcode Start Base" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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232 <param argument="--soloCBlen" type="integer" min="1" value="16" label="Cell Barcode Length" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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233 <param argument="--soloUMIstart" type="integer" min="1" value="17" label="UMI Start Base" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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234 <param argument="--soloUMIlen" type="integer" min="1" value="10" label="UMI Length" />
10
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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235 <conditional name="bccdna_mate" >
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236 <param name="bc_location" type="select" label="Barcode and cDNA on the same mate\?" >
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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237 <option value="other_mate" selected="true">BC and cDNA are on different mates of paired-end read</option>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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238 <option value="same_mate">BC and cDNA are on the same mate of paired-end read</option>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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239 </param>
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240 <when value="other_mate" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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241 <when value="same_mate" >
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242 <param argument="--soloBarcodeMate" type="select" label="Barcode sequence is a part of">
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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243 <option value="1" selected="true">mate 1</option>
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244 <option value="2">mate 2</option>
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245 </param>
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246 <param name="clip_n_bases" type="integer" value="39" label="Number of bases to clip (=CB+UMI+adapter)"/>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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247 </when>
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248 </conditional>
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249 <expand macro="solo_adapter_params" />
9
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250 </when>
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251 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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252 <param argument="--soloBarcodeReadLength" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Barcode Size is same size of the Read" help="Disable this if your R1 barcodes contain poly-T bases after the barcode sequence." />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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253 <conditional name="umidedup">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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254 <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs.">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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255 <expand macro="umidedup_options" />
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256 <option value="Exact" >Exact</option>
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257 <option value="1MM_CR" >CellRanger2-4 algorithm</option>
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258 </param>
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259 <when value="1MM_All"/>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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260 <when value="1MM_Directional_UMItools"/>
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261 <when value="1MM_Directional"/>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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262 <when value="Exact"/>
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263 <when value="1MM_CR">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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264 <param argument="--soloUMIfiltering" type="select" label="Type of UMI filtering" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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265 <option value="-" selected="true">Remove UMIs with N and homopolymers (similar to CellRanger 2.2.0)</option>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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266 <option value="MultiGeneUMI" >Remove lower-count UMIs that map to more than one gene</option>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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267 <option value="MultiGeneUMI_All" >Remove all UMIs that map to more than one gene</option>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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268 <option value="MultiGeneUMI_CR" >Remove lower-count UMIs that map to more than one gene, matching CellRanger > 3.0.0</option>
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269 </param>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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270 </when>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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271 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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272 <param argument="--soloCBmatchWLtype" type="select" label="Matching the Cell Barcodes to the WhiteList" help="Exact: only exact matches allowed; 1MM: only one match in whitelist with 1 mismatched base allowed. Allowed
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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273 CBs have to have at least one read with exact match; 1MM_multi: multiple matches in whitelist with 1 mismatched base allowed, posterior probability calculation is used choose one of the matches; 1MM_multi_pseudocounts: same as 1MM_Multi, but pseudocounts of 1 are added to all whitelist barcodes.">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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274 <expand macro="cb_match_wl_common" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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275 <expand macro="cb_match_wl_cellranger" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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276 </param>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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277 </when>
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278 <when value="CB_UMI_Complex">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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279 <expand macro="input_selection" />
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280 <repeat name="cb_whitelists" title="Cell barcode whitelist information" max="2" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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281 <param name="whitelist_file" format="txt,tsv" type="data" label="RNA-Seq Cell Barcode Whitelist"/>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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282 <param name="cb_start_anchor" type="select" label="Start anchor base for cell barcode">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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283 <expand macro="anchor_types" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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284 </param>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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285 <param name="cb_start_anchor_pos" type="integer" value="0" label="0-based position of the CB start with respect to the anchor base" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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286 <param name="cb_end_anchor" type="select" label="End anchor base for cell barcode">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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287 <expand macro="anchor_types" />
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288 </param>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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289 <param name="cb_end_anchor_pos" type="integer" value="0" label="0-based position of the CB end with respect to the anchor base" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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290 </repeat>
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291 <param name="umi_start_anchor" type="select" label="Start anchor base for UMI">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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292 <expand macro="anchor_types" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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293 </param>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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294 <param name="umi_start_anchor_pos" type="integer" value="0" label="0-based position of the UMI start with respect to the anchor base" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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295 <param name="umi_end_anchor" type="select" label="End anchor base for UMI">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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296 <expand macro="anchor_types" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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297 </param>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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298 <param name="umi_end_anchor_pos" type="integer" value="0" label="0-based position of the UMI end with respect to the anchor base" />
10
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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299 <expand macro="solo_adapter_params" />
13
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300 <conditional name="umidedup">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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301 <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs.">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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302 <expand macro="umidedup_options" />
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303 <option value="Exact" >Exact</option>
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304 <option value="1MM_CR" >CellRanger2-4 algorithm</option>
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305 </param>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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306 <when value="1MM_All"/>
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307 <when value="1MM_Directional_UMItools"/>
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308 <when value="1MM_Directional"/>
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309 <when value="Exact"/>
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310 <when value="1MM_CR">
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311 <param argument="--soloUMIfiltering" type="select" label="Type of UMI filtering" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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312 <option value="-" selected="true">Remove UMIs with N and homopolymers (similar to CellRanger 2.2.0)</option>
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313 <option value="MultiGeneUMI" >Remove lower-count UMIs that map to more than one gene</option>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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314 <option value="MultiGeneUMI_All" >Remove all UMIs that map to more than one gene</option>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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315 <option value="MultiGeneUMI_CR" >Remove lower-count UMIs that map to more than one gene, matching CellRanger > 3.0.0</option>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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316 </param>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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317 </when>
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318 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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319 <param argument="--soloCBmatchWLtype" type="select" label="Matching the Cell Barcodes to the WhiteList" help="Exact: only exact matches allowed; 1MM: only one match in whitelist with 1 mismatched base allowed. Allowed
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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320 CBs have to have at least one read with exact match; 1MM_multi: multiple matches in whitelist with 1 mismatched base allowed, posterior probability calculation is used choose one of the matches; 1MM_multi_pseudocounts: same as 1MM_Multi, but pseudocounts of 1 are added to all whitelist barcodes.">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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321 <expand macro="cb_match_wl_common" />
13
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parents: 12
diff changeset
322 <!-- should we add EditDist_2? -->
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parents: 8
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323 </param>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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parents: 8
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324 </when>
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325 <when value="SmartSeq">
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parents: 8
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326 <expand macro="input_selection_smart_seq" />
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327 <param name="cell_ids" format="txt,tsv" type="data" label="File containing cell IDs of the samples. One ID per line in order of samples in the above collection."/>
13
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parents: 12
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328 <conditional name="umidedup">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 12
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329 <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs.">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 12
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330 <expand macro="umidedup_options" />
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331 <option value="Exact" >Exact</option>
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parents: 13
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332 <option value="NoDedup" >Do not deduplicate UMIs</option>
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parents: 12
diff changeset
333 </param>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 12
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334 <when value="1MM_All"/>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 12
diff changeset
335 <when value="1MM_Directional_UMItools"/>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 12
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336 <when value="1MM_Directional"/>
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parents: 12
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337 <when value="Exact"/>
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parents: 12
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338 <when value="NoDedup"/>
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parents: 12
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339 </conditional>
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parents: 8
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340 </when>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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341 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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342 <section name="solo" title="Advanced Settings" expanded="true">
0
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343 <param argument="--soloStrand" type="select" label="Strandedness of Library" help="Unstranded has no strand information, Forward has the read strand the same as the original RNA molecule, Reverse has the read strand opposite to the original RNA molecule">
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344 <option value="Unstranded" >No strand information</option>
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345 <option value="Forward" selected="true" >Read strand same as the original RNA molecule</option>
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parents: 10
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346 <option value="Reverse" >Read strand opposite to the original RNA molecule</option>
0
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347 </param>
4
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parents: 3
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348 <param argument="--soloFeatures" type="select" label="Collect UMI counts for these genomic features" >
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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349 <option value="Gene" selected="true">Gene: Count reads matching the Gene Transcript</option>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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350 <option value="SJ" >Splice Junctions: Count reads at exon-intron junctions</option>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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351 <option value="GeneFull" >Full: Count all reads overlapping genes' exons and introns</option>
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parents: 12
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352 <option value="GeneFull_ExonOverIntron" >Full: Count all reads overlapping genes' exons and introns: prioritize 100% overlap with exons</option>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 12
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353 <option value="GeneFull_Ex50pAS" >Full: Count all reads overlapping genes' exons and introns: prioritize 50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction.</option>
0
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354 </param>
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355 <conditional name="filter" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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356 <param name="filter_type" type="select" label="Cell filtering type and parameters" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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357 <option value="cellranger2" selected="true" >Simple filtering of CellRanger v2</option>
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358 <option value="emptydrops" >EmptyDrops filtering in CellRanger flavor</option>
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359 <option value="topcells" >Filter top N cells</option>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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360 <option value="no_filter" >Do not filter</option>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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361 </param>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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parents: 8
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362 <when value="cellranger2" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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363 <param name="n_expected" type="integer" min="1" value="3000" label="Number of expected cells" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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364 <param name="max_perc" type="float" min="0" max="1" value="0.99" label="Robust maximum percentile for UMI count" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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365 <param name="max_min_ratio" type="float" min="1" value="10" label="Maximum to minimum ratio for UMI count" />
13
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parents: 12
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366 <param name="output_raw" type="boolean" checked="false" label="Output raw matrix in addition to filtered one" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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367 </when>
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parents: 9
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368 <when value="emptydrops" >
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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369 <param name="nExpectedCells" type="integer" min="1" value="3000" label="Number of expected cells" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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370 <param name="maxPercentile" type="float" min="0" max="1" value="0.99" label="Robust maximum percentile for UMI count" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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371 <param name="maxMinRatio" type="float" min="1" value="10" label="Maximum to minimum ratio for UMI count" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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372 <param name="indMin" type="integer" value="45000" label="Minimum number of barcodes (used as partition parameter for ambient estimation)" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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373 <param name="indMax" type="integer" value="90000" label="Maximum number of barcodes (used as partition parameter for ambient estimation)" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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374 <param name="umiMin" type="integer" value="500" label="Consider at least these many UMIs per barcode after initial cell calling" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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375 <param name="umiMinFracMedian" type="float" value="0.01" label="Minimum UMI:median ratio after initial cell calling" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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376 <param name="candMaxN" type="integer" value="20000" label="Number of extra barcodes after initial cell calling" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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377 <param name="FDR" type="float" value="0.01" label="Maximum adjusted p-value for determining a barcode as non-ambient" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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378 <param name="simN" type="integer" value="10000" label="Number of log likelihood simulations" />
13
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379 <param name="output_raw" type="boolean" checked="false" label="Output raw matrix in addition to filtered one" />
10
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380 </when>
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381 <when value="topcells" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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382 <param name="n_cells" type="integer" min="1" value="3000" label="Number of top cells to report sorted by UMI count" />
13
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parents: 12
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383 <param name="output_raw" type="boolean" checked="false" label="Output raw matrix in addition to filtered one" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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parents: 8
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384 </when>
13
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parents: 12
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385 <when value="no_filter">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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386 <param name="output_raw" type="hidden" value="true" />
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387 </when>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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388 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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389 <param argument="--soloOutFormatFeaturesGeneField3" type="text" value="Gene Expression" label="Field 3 in the Genes output." help="Input '-' to remove the 3rd column from the output." />
13
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390 <param argument="--outSAMattributes" type="select" display="checkboxes" multiple="true" optional="true"
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 12
diff changeset
391 label="Read alignment tags to include in the BAM output">
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parents: 12
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392 <expand macro="common_SAM_attributes"/>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 12
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393 <option value="CR">CR Cellular barcode sequence bases (uncorrected)</option>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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diff changeset
394 <option value="CY">CY Phred quality of the cellular barcode sequence in the CR tag</option>
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parents: 13
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395 <option value="UR">UR UMI (uncorrected)</option>
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396 <option value="UY">UY Phred quality of the UMI</option>
13
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parents: 12
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397 <option value="GX">GX Gene ID</option>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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398 <option value="GN">GN Gene name</option>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
399 <option value="CB">CB Cell identifier (corrected)</option>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
400 <option value="UB">UB UMI (corrected)</option>
14
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
401 <option value="sM">sM assessment of CB and UMI</option>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
402 <option value="sS">sS sequence of the entire barcode (CB,UMI,adapter...)</option>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
403 <option value="sQ">quality of the entire barcode</option>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
404 </param>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
405 <param name="quantModeGene" type="boolean" truevalue="GeneCounts" falsevalue="" checked="false" label="Output global gene count" help="Can be used by MultiQC" />
14
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
406 <param argument="--outSAMunmapped" type="boolean" truevalue="--outSAMunmapped Within" falsevalue="--outSAMunmapped None" checked="false" label="Output unmapped reads in the BAM" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
407 <expand macro="outSAMmapqUnique"/>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
408 <expand macro="limits" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
409 </section>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
410 <expand macro="outWig"/>
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
411 </inputs>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
412 <outputs>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
413 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out">
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
414 <expand macro="dbKeyActions" />
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
415 </data>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
416 <!--
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
417 <data format="tsv" name="output_genes" label="${tool.name} on ${on_string}: Genes" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
418 <data format="tsv" name="output_barcodes" label="${tool.name} on ${on_string}: Barcodes" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
419 <data format="mtx" name="output_matrix" label="${tool.name} on ${on_string}: Matrix Gene Counts" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
420 <expand macro="dbKeyActions" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
421 </data>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
422 -->
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
423 <!-- soloCellFilter set to None, if SJ is selected for soloFeatures -->
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
424 <data format="tsv" name="output_genes" label="${tool.name} on ${on_string}: Genes raw"
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
425 from_work_dir="Solo.out/soloFeatures/raw/features.tsv" >
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
426 <filter>solo['filter']['output_raw'] or solo['soloFeatures'] == "SJ" </filter>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
427 </data>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
428 <data format="tsv" name="output_genes_filtered" label="${tool.name} on ${on_string}: Genes filtered"
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
429 from_work_dir="Solo.out/soloFeatures/filtered/features.tsv" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
430 <filter>solo['filter']['filter_type'] != "no_filter" and solo['soloFeatures'] != "SJ" </filter>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
431 </data>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
432 <data format="tsv" name="output_barcodes" label="${tool.name} on ${on_string}: Barcodes raw"
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
433 from_work_dir="Solo.out/soloFeatures/raw/barcodes.tsv" >
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
434 <filter>solo['filter']['output_raw'] or solo['soloFeatures'] == "SJ" </filter>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
435 </data>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
436 <data format="tsv" name="output_barcodes_filtered" label="${tool.name} on ${on_string}: Barcodes filtered"
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
437 from_work_dir="Solo.out/soloFeatures/filtered/barcodes.tsv" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
438 <filter>solo['filter']['filter_type'] != "no_filter" and solo['soloFeatures'] != "SJ" </filter>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
439 </data>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
440 <data format="mtx" name="output_matrix" label="${tool.name} on ${on_string}: Matrix Gene Counts raw"
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
441 from_work_dir="Solo.out/soloFeatures/raw/matrix.mtx" >
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
442 <filter>solo['soloFeatures'] == "Gene" and solo['filter']['output_raw'] </filter>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
443 <expand macro="dbKeyActions" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
444 </data>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
445 <data format="mtx" name="output_matrix_filtered" label="${tool.name} on ${on_string}: Matrix Gene Counts filtered"
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
446 from_work_dir="Solo.out/soloFeatures/filtered/matrix.mtx" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
447 <filter>solo['soloFeatures'] == "Gene" and solo['filter']['filter_type'] != "no_filter" </filter>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
448 <expand macro="dbKeyActions" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
449 </data>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
450 <data format="mtx" name="output_matrixSJ" label="${tool.name} on ${on_string}: Matrix Splice Junction Counts"
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
451 from_work_dir="Solo.out/soloFeatures/raw/matrix.mtx" >
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
452 <filter>solo['soloFeatures'] == "SJ" </filter>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
453 <expand macro="dbKeyActions" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
454 </data>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
455 <data format="mtx" name="output_matrixGeneFull" label="${tool.name} on ${on_string}: Matrix Full Gene Counts raw"
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
456 from_work_dir="Solo.out/soloFeatures/raw/matrix.mtx" >
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
457 <filter>"GeneFull" in solo['soloFeatures'] and solo['filter']['output_raw'] </filter>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
458 <expand macro="dbKeyActions" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
459 </data>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
460 <data format="mtx" name="output_matrixGeneFull_filtered" label="${tool.name} on ${on_string}: Matrix Full Gene Counts filtered"
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
461 from_work_dir="Solo.out/soloFeatures/filtered/matrix.mtx" >
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
462 <filter>"GeneFull" in solo['soloFeatures'] and solo['filter']['filter_type'] != "no_filter" </filter>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
463 <expand macro="dbKeyActions" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
464 </data>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
465 <data format="bam" name="output_BAM" label="${tool.name} on ${on_string}: Alignments" >
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
466 <expand macro="dbKeyActions" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
467 </data>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
468 <data format="txt" name="output_stats" label="${tool.name} on ${on_string}: Barcode/Feature Statistic Summaries"/>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
469 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: combined reads per gene" from_work_dir="ReadsPerGene.out.tab">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
470 <filter>solo['quantModeGene']</filter>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
471 <expand macro="outCountActions" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
472 </data>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
473 <expand macro="outWigOutputs"/>
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
474 </outputs>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
475 <!-- Generating test data that is big enough for STARsolo to detect and small enough
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
476 for Galaxy to test requires careful modification of input FASTA and GTF data,
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
477 where the length of FASTA cannot exceed the largest position in the GTF file,
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
478 regardless of the FASTA starting sequence position.
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
479
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
480 A full writeup of how to subset single cell data for use in STARsolo is given
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
481 here: https://gist.github.com/mtekman/149a7c52fd73e5d8ebe49f5a27b0743d
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
482 -->
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
483 <tests>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
484 <test expect_num_outputs="7">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
485 <!-- test 1 -->
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
486 <conditional name="refGenomeSource">
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
487 <param name="geneSource" value="history" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
488 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
2
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
489 <param name="genomeSAindexNbases" value="4" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
490 <param name="sjdbOverhang" value="100" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
491 <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
492 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
493 <conditional name="sc" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
494 <param name="solo_type" value="CB_UMI_Simple" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
495 <conditional name="input_types">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
496 <param name="use" value="repeat" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
497 <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
498 <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
499 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
500 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
501 <conditional name="params">
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
502 <param name="chemistry" value="Cv3" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
503 </conditional>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
504 <conditional name="umidedup">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
505 <param name="soloUMIdedup" value="1MM_All" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
506 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
507 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
508 <section name="solo" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
509 <conditional name="filter">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
510 <param name="filter_type" value="no_filter" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
511 </conditional>
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
512 <param name="soloStrand" value="Forward" />
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
513 <param name="soloFeatures" value="Gene" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
514 <param name="quantModeGene" value="true" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
515 </section>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
516 <output name="output_barcodes" >
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
517 <assert_contents>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
518 <!-- first and last line -->
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
519 <has_line line="AAACCTGAGCGCTCCA" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
520 <has_line line="TTTGGTTAGTGGGCTA" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
521 <has_n_lines n="394" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
522 </assert_contents>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
523 </output>
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
524 <output name="output_genes">
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
525 <assert_contents>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
526 <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
527 <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
528 <has_n_lines n="14" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
529 </assert_contents>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
530 </output>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
531 <output name="output_matrix" >
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
532 <assert_contents>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
533 <has_line_matching expression="14\s+394\s+7" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
534 <has_line_matching expression="4\s+381\s+1" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
535 <has_n_lines n="10" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
536 </assert_contents>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
537 </output>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
538 <output name="output_stats" >
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
539 <assert_contents>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
540 <has_line_matching expression="\s+noUnmapped\s+5823" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
541 <has_line_matching expression="\s+yesUMIs\s+8" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
542 </assert_contents>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
543 </output>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
544 <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
545 <output name="reads_per_gene" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
546 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
547 <has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
548 <has_line_matching expression="ENSG00000275464\s+38\s+1\s+40" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
549 </assert_contents>
14
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
550 <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
551 </output>
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
552 </test>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
553 <test expect_num_outputs="6">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
554 <!-- test 2 -->
14
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
555 <!-- same as above, but using custom, no reads_per_gene and include unmapped reads-->
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
556 <conditional name="refGenomeSource">
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
557 <param name="geneSource" value="history" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
558 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
2
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
559 <param name="genomeSAindexNbases" value="4" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
560 <param name="sjdbOverhang" value="100" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
561 <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
2
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
562 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
563 <conditional name="sc" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
564 <param name="solo_type" value="CB_UMI_Simple" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
565 <conditional name="input_types">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
566 <param name="use" value="repeat" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
567 <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
568 <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
569 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
570 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
2
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
571 <conditional name="params">
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
572 <param name="chemistry" value="custom" />
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
573 <param name="soloCBstart" value="1" />
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
574 <param name="soloCBlen" value="16" />
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
575 <param name="soloUMIstart" value="17" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
576 <param name="soloUMIlen" value="12" />
2
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
577 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
578 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
579 <section name="solo" >
2
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
580 <param name="soloStrand" value="Forward" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
581 <param name="soloFeatures" value="Gene" />
14
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
582 <param name="outSAMunmapped" value="true" />
5
c23da6257d6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2082c018009fa73c4afee8313febab13bb807ea8"
iuc
parents: 4
diff changeset
583 </section>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
584 <output name="output_barcodes_filtered" >
5
c23da6257d6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2082c018009fa73c4afee8313febab13bb807ea8"
iuc
parents: 4
diff changeset
585 <assert_contents>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
586 <!-- first and last line -->
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
587 <has_line line="ACACCGGTCTAACGGT" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
588 <has_line line="TTCTCAATCCACGTTC" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
589 <has_n_lines n="7" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
590 </assert_contents>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
591 </output>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
592 <output name="output_genes_filtered">
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
593 <assert_contents>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
594 <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
595 <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
596 <has_n_lines n="14" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
597 </assert_contents>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
598 </output>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
599 <output name="output_matrix_filtered" >
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
600 <assert_contents>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
601 <has_line_matching expression="14\s+7\s+7" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
602 <has_line_matching expression="4\s+7\s+1" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
603 <has_n_lines n="10" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
604 </assert_contents>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
605 </output>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
606 <output name="output_stats" >
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
607 <assert_contents>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
608 <has_line_matching expression="\s+noUnmapped\s+5823" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
609 <has_line_matching expression="\s+yesUMIs\s+8" />
5
c23da6257d6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2082c018009fa73c4afee8313febab13bb807ea8"
iuc
parents: 4
diff changeset
610 </assert_contents>
c23da6257d6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2082c018009fa73c4afee8313febab13bb807ea8"
iuc
parents: 4
diff changeset
611 </output>
14
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
612 <output name="output_BAM">
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
613 <assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
614 <has_size value="884669" delta="80000" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
615 </assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
616 </output>
5
c23da6257d6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2082c018009fa73c4afee8313febab13bb807ea8"
iuc
parents: 4
diff changeset
617 </test>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
618 <test expect_num_outputs="6">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
619 <!-- test 3 -->
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
620 <!-- Multiple repeats test -->
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
621 <conditional name="refGenomeSource">
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
622 <param name="geneSource" value="history" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
623 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
624 <param name="genomeSAindexNbases" value="4" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
625 <param name="sjdbOverhang" value="100" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
626 <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
627 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
628 <conditional name="sc" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
629 <param name="solo_type" value="CB_UMI_Simple" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
630 <conditional name="input_types">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
631 <param name="use" value="repeat" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
632 <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz,pbmc_1k_v2_L001.R1.10k.fastq.gz,pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
633 <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz,pbmc_1k_v2_L001.R2.10k.fastq.gz,pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
634 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
635 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
636 <conditional name="params">
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
637 <param name="chemistry" value="Cv3" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
638 </conditional>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
639 <conditional name="umidedup">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
640 <param name="soloUMIdedup" value="1MM_All" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
641 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
642 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
643 <section name="solo" >
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
644 <param name="soloStrand" value="Forward" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
645 <param name="soloFeatures" value="Gene" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
646 </section>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
647 <output name="output_barcodes_filtered" >
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
648 <assert_contents>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
649 <has_line line="ACACCGGTCTAACGGT" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
650 <has_line line="TTCTCAATCCACGTTC" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
651 <has_n_lines n="7" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
652 </assert_contents>
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
653 </output>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
654 <output name="output_BAM" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
655 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
656 <has_size value="166147" delta="600" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
657 </assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
658 </output>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
659 </test>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
660 <test expect_num_outputs="10">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
661 <!-- test 4 -->
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
662 <!-- Test with paired collection -->
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
663 <conditional name="refGenomeSource">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
664 <param name="geneSource" value="history" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
665 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
666 <param name="genomeSAindexNbases" value="4" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
667 <param name="sjdbOverhang" value="100" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
668 <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
669 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
670 <conditional name="sc" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
671 <param name="solo_type" value="CB_UMI_Simple" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
672 <conditional name="input_types">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
673 <param name="use" value="list_paired" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
674 <param name="input_collection" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
675 <collection type="paired">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
676 <element name="forward" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
677 <element name="reverse" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
678 </collection>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
679 </param>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
680 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
681 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
682 <conditional name="params">
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
683 <param name="chemistry" value="Cv3" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
684 </conditional>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
685 <conditional name="umidedup">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
686 <param name="soloUMIdedup" value="1MM_All" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
687 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
688 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
689 <section name="solo" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
690 <param name="soloStrand" value="Forward" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
691 <param name="soloFeatures" value="Gene" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
692 </section>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
693 <conditional name="outWig">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
694 <param name="outWigType" value="bedGraph" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
695 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
696 <output name="output_barcodes_filtered" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
697 <assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
698 <has_line line="ACACCGGTCTAACGGT" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
699 <has_line line="TTCTCAATCCACGTTC" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
700 <has_n_lines n="7" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
701 </assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
702 </output>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
703 <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
704 <output name="signal_unique_str1" file="Signal.Unique.str1.out.bg" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
705 <output name="signal_uniquemultiple_str1" file="Signal.UniqueMultiple.str1.out.bg" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
706 <output name="signal_unique_str2" file="Signal.Unique.str2.out.bg" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
707 <output name="signal_uniquemultiple_str2" file="Signal.UniqueMultiple.str2.out.bg" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
708 </test>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
709 <test expect_num_outputs="9">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
710 <!-- test 5 -->
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
711 <!-- Test soloFeatures, soloCBmatchWLtype, soloCellFilter, soloOutFormatFeaturesGeneField3 -->
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
712 <conditional name="refGenomeSource">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
713 <param name="geneSource" value="history" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
714 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
715 <param name="genomeSAindexNbases" value="4" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
716 <param name="sjdbOverhang" value="100" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
717 <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
5
c23da6257d6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2082c018009fa73c4afee8313febab13bb807ea8"
iuc
parents: 4
diff changeset
718 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
719 <conditional name="sc" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
720 <param name="solo_type" value="CB_UMI_Simple" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
721 <conditional name="input_types">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
722 <param name="use" value="repeat" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
723 <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
724 <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
725 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
726 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
727 <param name="soloCBmatchWLtype" value="1MM_multi_pseudocounts" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
728 <conditional name="params">
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
729 <param name="chemistry" value="Cv3" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
730 </conditional>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
731 <conditional name="umidedup">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
732 <param name="soloUMIdedup" value="1MM_All" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
733 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
734 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
735 <section name="solo" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
736 <param name="soloStrand" value="Forward" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
737 <param name="soloFeatures" value="GeneFull" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
738 <conditional name="filter">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
739 <param name="filter_type" value="topcells" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
740 <param name="n_cells" value="5" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
741 <param name="output_raw" value="true" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
742 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
743 <param name="soloOutFormatFeaturesGeneField3" value="Dummy Text" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
744 </section>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
745 <output name="output_barcodes_filtered" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
746 <assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
747 <!-- first and last line -->
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
748 <has_line line="AGACGTTCAAGGCTCC" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
749 <has_line line="TCAACGAAGCTAGTGG" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
750 <has_n_lines n="6" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
751 </assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
752 </output>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
753 <output name="output_genes_filtered" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
754 <assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
755 <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Dummy\s+Text" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
756 <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Dummy\s+Text" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
757 <has_n_lines n="14" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
758 </assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
759 </output>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
760 <output name="output_matrixGeneFull_filtered" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
761 <assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
762 <has_line_matching expression="14\s+6\s+14" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
763 <has_line_matching expression="10\s+6\s+1" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
764 <has_n_lines n="17" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
765 </assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
766 </output>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
767 <output name="output_barcodes" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
768 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
769 <!-- first and last line -->
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
770 <has_line line="AAACCTGAGCGCTCCA" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
771 <has_line line="TTTGGTTAGTGGGCTA" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
772 <has_n_lines n="394" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
773 </assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
774 </output>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
775 <output name="output_genes">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
776 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
777 <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Dummy\s+Text" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
778 <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Dummy\s+Text" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
779 <has_n_lines n="14" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
780 </assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
781 </output>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
782 <output name="output_matrix" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
783 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
784 <has_line_matching expression="14\s+394\s+195" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
785 <has_line_matching expression="3\s+1\s+1" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
786 <has_n_lines n="198" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
787 </assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
788 </output>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
789 </test>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
790 <test expect_num_outputs="6">
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
791 <!-- test 6 -->
10
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
792 <!-- Emptydrops filtering -->
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
793 <conditional name="refGenomeSource">
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
794 <param name="geneSource" value="history" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
795 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
796 <param name="genomeSAindexNbases" value="4" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
797 <param name="sjdbOverhang" value="100" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
798 <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
799 </conditional>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
800 <conditional name="sc" >
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
801 <param name="solo_type" value="CB_UMI_Simple" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
802 <conditional name="input_types">
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
803 <param name="use" value="repeat" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
804 <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
805 <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
806 </conditional>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
807 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
808 <conditional name="params">
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
809 <param name="chemistry" value="Cv3" />
10
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
810 </conditional>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
811 <conditional name="umidedup">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
812 <param name="soloUMIdedup" value="1MM_All" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
813 </conditional>
10
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
814 </conditional>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
815 <section name="solo" >
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
816 <conditional name="filter">
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
817 <param name="filter_type" value="emptydrops" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
818 <param name="nExpectedCells" value="5" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
819 <param name="maxPercentile" value="0.99" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
820 <param name="maxMinRatio" value="10" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
821 <param name="indMin" value="45000" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
822 <param name="indMax" value="90000" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
823 <param name="umiMin" value="500" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
824 <param name="umiMinFracMedian" value="0.01" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
825 <param name="candMaxN" value="20000" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
826 <param name="FDR" value="0.01" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
827 <param name="simN" value="10000" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
828 </conditional>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
829 <param name="soloStrand" value="Forward" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
830 <param name="soloFeatures" value="Gene" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
831 </section>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
832 <output name="output_barcodes_filtered">
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
833 <assert_contents>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
834 <!-- first and last line -->
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
835 <has_line line="ACACCGGTCTAACGGT" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
836 <has_line line="TTCTCAATCCACGTTC" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
837 <has_n_lines n="7" />
10
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
838 </assert_contents>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
839 </output>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
840 <output name="output_genes_filtered">
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
841 <assert_contents>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
842 <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
843 <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
844 <has_n_lines n="14" />
10
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
845 </assert_contents>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
846 </output>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
847 <output name="output_matrix_filtered" >
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
848 <assert_contents>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
849 <has_line_matching expression="14\s+7\s+7" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
850 <has_line_matching expression="4\s+7\s+1" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
851 <has_n_lines n="10" />
10
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
852 </assert_contents>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
853 </output>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
854 <output name="output_stats" >
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
855 <assert_contents>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
856 <has_line_matching expression="\s+noUnmapped\s+5823" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
857 <has_line_matching expression="\s+yesUMIs\s+8" />
10
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
858 </assert_contents>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
859 </output>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
860 <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
861 </test>
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
862 <test expect_num_outputs="6">
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
863 <!-- test 7 -->
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
864 <!-- Test soloType CB_UMI_Complex -->
2
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
865 <conditional name="refGenomeSource">
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
866 <param name="geneSource" value="history" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
867 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
2
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 0
diff changeset
868 <param name="genomeSAindexNbases" value="4" />
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
869 <param name="sjdbOverhang" value="100" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
870 <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
871 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
872 <conditional name="sc" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
873 <param name="solo_type" value="CB_UMI_Complex" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
874 <conditional name="input_types">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
875 <param name="use" value="repeat" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
876 <param name="input1" value="indrop.R1.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
877 <param name="input2" value="indrop.R2.fastq.gz" ftype="fastqsanger.gz" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
878 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
879 <repeat name="cb_whitelists" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
880 <param name="whitelist_file" value="indrop.barcodes1.txt"/>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
881 <param name="cb_start_anchor" value="0" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
882 <param name="cb_start_anchor_pos" value="0" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
883 <param name="cb_end_anchor" value="2" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
884 <param name="cb_end_anchor_pos" value="-1" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
885 </repeat>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
886 <repeat name="cb_whitelists" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
887 <param name="whitelist_file" value="indrop.barcodes2.txt"/>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
888 <param name="cb_start_anchor" value="3" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
889 <param name="cb_start_anchor_pos" value="1" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
890 <param name="cb_end_anchor" value="3" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
891 <param name="cb_end_anchor_pos" value="8" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
892 </repeat>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
893 <param name="umi_start_anchor" value="3" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
894 <param name="umi_start_anchor_pos" value="9" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
895 <param name="umi_end_anchor" value="3" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
896 <param name="umi_end_anchor_pos" value="14" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
897 <param name="soloAdapterSequence" value="GAGTGATTGCTTGTGACGCCTT" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
898 <param name="soloAdapterMismatchesNmax" value="1" />
10
a6fba3d92531 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 9
diff changeset
899 <param name="clipAdapterType" value="CellRanger4" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
900 <conditional name="umidedup">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
901 <param name="soloUMIdedup" value="1MM_All" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
902 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
903 <param name="soloCBmatchWLtype" value="1MM" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
904 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
905 <output name="output_barcodes_filtered" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
906 <assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
907 <!-- first and last line -->
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
908 <has_line line="ACAACGTGG_AAACCTCC" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
909 <has_line line="ATTCCAGAC_TTCGCTGG" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
910 <has_n_lines n="33" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
911 </assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
912 </output>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
913 <output name="output_genes_filtered">
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
914 <assert_contents>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
915 <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
916 <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
917 <has_n_lines n="14" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
918 </assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
919 </output>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
920 <output name="output_matrix_filtered" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
921 <assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
922 <has_line_matching expression="14\s+33\s+36" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
923 <has_line_matching expression="2\s+33\s+1" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
924 <has_n_lines n="39" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
925 </assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
926 </output>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
927 <output name="output_stats" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
928 <assert_contents>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
929 <has_line_matching expression="\s+yesWLmatchExact\s+791" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
930 <has_line_matching expression="\s+yesUMIs\s+36" />
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
931 </assert_contents>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
932 </output>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
933 </test>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
934 <test expect_num_outputs="6">
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
935 <!-- test 8 -->
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
936 <!-- Test soloType SmartSeq -->
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
937 <conditional name="refGenomeSource">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
938 <param name="geneSource" value="history" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
939 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
940 <param name="genomeSAindexNbases" value="4" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
941 <param name="sjdbOverhang" value="100" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
942 <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
943 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
944 <conditional name="sc" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
945 <param name="solo_type" value="SmartSeq" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
946 <conditional name="input_types_smart_seq">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
947 <param name="use" value="list_paired_end" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
948 <param name="paired_end_collection" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
949 <collection type="list:paired">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
950 <element name="pair1">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
951 <collection type="paired">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
952 <element name="forward" value="smartseq1.R1.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
953 <element name="reverse" value="smartseq1.R2.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
954 </collection>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
955 </element>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
956 <element name="pair2">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
957 <collection type="paired">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
958 <element name="forward" value="smartseq2.R1.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
959 <element name="reverse" value="smartseq2.R2.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
960 </collection>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
961 </element>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
962 <element name="pair3">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
963 <collection type="paired">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
964 <element name="forward" value="smartseq3.R1.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
965 <element name="reverse" value="smartseq3.R2.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
966 </collection>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
967 </element>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
968 <element name="pair4">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
969 <collection type="paired">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
970 <element name="forward" value="smartseq4.R1.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
971 <element name="reverse" value="smartseq4.R2.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
972 </collection>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
973 </element>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
974 <element name="pair5">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
975 <collection type="paired">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
976 <element name="forward" value="smartseq5.R1.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
977 <element name="reverse" value="smartseq5.R2.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
978 </collection>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
979 </element>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
980 <element name="pair6">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
981 <collection type="paired">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
982 <element name="forward" value="smartseq6.R1.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
983 <element name="reverse" value="smartseq6.R2.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
984 </collection>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
985 </element>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
986 <element name="pair7">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
987 <collection type="paired">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
988 <element name="forward" value="smartseq7.R1.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
989 <element name="reverse" value="smartseq7.R2.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
990 </collection>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
991 </element>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
992 <element name="pair8">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
993 <collection type="paired">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
994 <element name="forward" value="smartseq8.R1.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
995 <element name="reverse" value="smartseq8.R2.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
996 </collection>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
997 </element>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
998 <element name="pair9">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
999 <collection type="paired">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1000 <element name="forward" value="smartseq9.R1.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1001 <element name="reverse" value="smartseq9.R2.fastq.gz" ftype="fastqsanger.gz" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1002 </collection>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1003 </element>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1004 </collection>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1005 </param>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1006 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1007 <param name="cell_ids" value="smartseq.cellids.txt" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1008 <conditional name="umidedup">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1009 <param name="soloUMIdedup" value="Exact" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1010 </conditional>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1011 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1012 <section name="solo" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1013 <param name="soloStrand" value="Unstranded" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1014 <conditional name="filter">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1015 <param name="filter_type" value="topcells" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1016 <param name="n_cells" value="2" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1017 </conditional>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1018 </section>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1019 <output name="output_barcodes_filtered" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1020 <assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1021 <has_line line="CSC6_D02" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1022 <not_has_text text="MGH26_A02" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1023 <has_n_lines n="3" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1024 </assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1025 </output>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1026 <output name="output_genes_filtered">
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1027 <assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1028 <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1029 <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1030 <has_n_lines n="14" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1031 </assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1032 </output>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1033 <output name="output_matrix_filtered" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1034 <assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1035 <has_line_matching expression="14\s+3\s+10" />
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1036 <has_line_matching expression="12\s+3\s+1" />
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1037 <has_n_lines n="13" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1038 </assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1039 </output>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1040 <output name="output_stats" >
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1041 <assert_contents>
13
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1042 <has_line_matching expression="\s+yesWLmatchExact\s+9000" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1043 <has_line_matching expression="\s+yesUMIs\s+32" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1044 </assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1045 </output>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1046 </test>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1047 <test expect_num_outputs="6">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1048 <!-- test 9 -->
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1049 <!-- Test outSAMattributes -->
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1050 <conditional name="refGenomeSource">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1051 <param name="geneSource" value="history" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1052 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1053 <param name="genomeSAindexNbases" value="4" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1054 <param name="sjdbOverhang" value="100" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1055 <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1056 </conditional>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1057 <conditional name="sc" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1058 <param name="solo_type" value="CB_UMI_Simple" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1059 <conditional name="input_types">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1060 <param name="use" value="repeat" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1061 <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1062 <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1063 </conditional>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1064 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1065 <conditional name="params">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1066 <param name="chemistry" value="Cv3" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1067 </conditional>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1068 <conditional name="umidedup">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1069 <param name="soloUMIdedup" value="1MM_All" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1070 </conditional>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1071 </conditional>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1072 <section name="solo" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1073 <conditional name="filter">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1074 <param name="filter_type" value="no_filter" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1075 </conditional>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1076 <param name="soloStrand" value="Forward" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1077 <param name="soloFeatures" value="Gene" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1078 <param name="outSAMattributes" value="NH,HI,AS,nM,GX,GN,CB,UB" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1079 </section>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1080 <output name="output_barcodes" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1081 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1082 <!-- first and last line -->
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1083 <has_line line="AAACCTGAGCGCTCCA" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1084 <has_line line="TTTGGTTAGTGGGCTA" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1085 <has_n_lines n="394" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1086 </assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1087 </output>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1088 <output name="output_genes">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1089 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1090 <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1091 <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1092 <has_n_lines n="14" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1093 </assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1094 </output>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1095 <output name="output_matrix" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1096 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1097 <has_line_matching expression="14\s+394\s+7" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1098 <has_line_matching expression="4\s+381\s+1" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1099 <has_n_lines n="10" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1100 </assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1101 </output>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1102 <output name="output_stats" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1103 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1104 <has_line_matching expression="\s+noUnmapped\s+5823" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1105 <has_line_matching expression="\s+yesUMIs\s+8" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1106 </assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1107 </output>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1108 <output name="output_BAM" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1109 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1110 <has_size value="153108" delta="600" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1111 </assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1112 </output>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1113 </test>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1114 <test expect_num_outputs="6">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1115 <!-- test 10 -->
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1116 <!-- Test soloFeatures -->
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1117 <conditional name="refGenomeSource">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1118 <param name="geneSource" value="history" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1119 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1120 <param name="genomeSAindexNbases" value="4" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1121 <param name="sjdbOverhang" value="100" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1122 <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1123 </conditional>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1124 <conditional name="sc" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1125 <param name="solo_type" value="CB_UMI_Simple" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1126 <conditional name="input_types">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1127 <param name="use" value="repeat" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1128 <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1129 <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1130 </conditional>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1131 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1132 <param name="soloCBmatchWLtype" value="1MM_multi_pseudocounts" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1133 <conditional name="params">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1134 <param name="chemistry" value="Cv3" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1135 </conditional>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1136 <conditional name="umidedup">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1137 <param name="soloUMIdedup" value="1MM_CR" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1138 <param name="soloUMIfiltering" value="MultiGeneUMI" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1139 </conditional>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1140 </conditional>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1141 <section name="solo" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1142 <param name="soloStrand" value="Forward" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1143 <param name="soloFeatures" value="GeneFull_ExonOverIntron" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1144 <conditional name="filter">
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1145 <param name="filter_type" value="no_filter" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1146 </conditional>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1147 <param name="soloOutFormatFeaturesGeneField3" value="Dummy Text" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1148 </section>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1149 <output name="output_barcodes" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1150 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1151 <!-- first and last line -->
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1152 <has_line line="AAACCTGAGCGCTCCA" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1153 <has_line line="TTTGGTTAGTGGGCTA" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1154 <has_n_lines n="394" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1155 </assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1156 </output>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1157 <output name="output_genes" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1158 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1159 <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Dummy\s+Text" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1160 <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Dummy\s+Text" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1161 <has_n_lines n="14" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1162 </assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1163 </output>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1164 <output name="output_matrixGeneFull" >
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1165 <assert_contents>
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1166 <has_line_matching expression="14\s+394\s+104" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1167 <has_line_matching expression="10\s+2\s+1" />
9ee34ba73ebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 12
diff changeset
1168 <has_n_lines n="107" />
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1169 </assert_contents>
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
1170 </output>
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1171 </test>
14
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1172 <test expect_num_outputs="7">
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1173 <!-- test 11 indexed -->
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1174 <conditional name="refGenomeSource">
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1175 <param name="geneSource" value="indexed" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1176 <conditional name="GTFconditional">
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1177 <param name="GTFselect" value="without-gtf-with-gtf" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1178 <param name="genomeDir" value="000" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1179 <param name="sjdbOverhang" value="75"/>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1180 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1181 </conditional>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1182 </conditional>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1183 <conditional name="sc" >
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1184 <param name="solo_type" value="CB_UMI_Simple" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1185 <conditional name="input_types">
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1186 <param name="use" value="repeat" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1187 <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1188 <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1189 </conditional>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1190 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1191 <conditional name="params">
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1192 <param name="chemistry" value="Cv3" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1193 </conditional>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1194 <conditional name="umidedup">
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1195 <param name="soloUMIdedup" value="1MM_All" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1196 </conditional>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1197 </conditional>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1198 <section name="solo" >
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1199 <conditional name="filter">
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1200 <param name="filter_type" value="no_filter" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1201 </conditional>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1202 <param name="soloStrand" value="Forward" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1203 <param name="soloFeatures" value="Gene" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1204 <param name="quantModeGene" value="true" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1205 </section>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1206 <output name="output_barcodes" >
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1207 <assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1208 <!-- first and last line -->
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1209 <has_line line="AAACCTGAGCGCTCCA" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1210 <has_line line="TTTGGTTAGTGGGCTA" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1211 <has_n_lines n="394" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1212 </assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1213 </output>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1214 <output name="output_genes">
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1215 <assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1216 <has_line_matching expression="GENE1\s+GENE1\s+Gene\s+Expression" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1217 <has_n_lines n="1" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1218 </assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1219 </output>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1220 <output name="output_matrix" >
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1221 <assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1222 <has_line_matching expression="1\s+394\s+31" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1223 <has_line_matching expression="1\s+2\s+1" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1224 <has_n_lines n="34" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1225 </assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1226 </output>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1227 <output name="output_stats" >
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1228 <assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1229 <has_line_matching expression="\s+noUnmapped\s+6335" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1230 <has_line_matching expression="\s+yesUMIs\s+33" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1231 </assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1232 </output>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1233 <output name="output_BAM">
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1234 <assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1235 <has_size value="7133" delta="1000"/>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1236 </assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1237 </output>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1238 <output name="reads_per_gene" >
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1239 <assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1240 <has_line_matching expression="GENE1\s+41\s+41\s+0" />
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1241 </assert_contents>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1242 </output>
1cd2511a396e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 13
diff changeset
1243 </test>
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1244 </tests>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1245 <help><![CDATA[
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1246 **What it does**
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1247
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
1248 **STARSolo** is a turnkey solution for analyzing droplet single cell RNA sequencing data (e.g. 10X Genomics Chromium System) built directly into STAR_ code. STARsolo takes raw FASTQ reads files as input, and performs the following operations:
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1249
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1250 * Error correction and demultiplexing of cell barcodes using user-input whitelist
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1251 * Mapping the reads to the reference genome using the standard STAR spliced read alignment algorithm
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1252 * Error correction and collapsing (deduplication) of Unique Molecular Identifiers (UMIs)
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1253 * Quantification of per-cell gene expression by counting the number of reads per gene
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1254
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1255 STARsolo output is designed to be a drop-in replacement for 10X CellRanger gene quantification output. It follows CellRanger logic for cell barcode whitelisting and UMI deduplication, and produces nearly identical gene counts in the same format. At the same time STARsolo is 10 times faster than CellRanger.
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1256
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 5
diff changeset
1257 .. _STAR: https://github.com/alexdobin/STAR
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1258 ]]></help>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1259 <expand macro="citations"/>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
1260 </tool>