Mercurial > repos > iuc > velocyto_cli

annotate velocyto_cli.xml @ 0:81ad264c1548 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
author iuc
date Sat, 13 May 2023 12:31:10 +0000
parents
children 4a75f9c84a4b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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1 <tool id="velocyto_cli" name="velocyto CLI" version="@VERSION@+galaxy0">
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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2 <description>pre-process data for the analysis of RNA velocity</description>
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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3 <macros>
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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4 <import>macros.xml</import>
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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5 </macros>
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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6 <expand macro="edam"/>
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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7 <expand macro="requirements"/>
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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8 <stdio>
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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9 <!-- Anything other than zero is an error -->
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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10 <exit_code level="fatal" range="1:"/>
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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11 <exit_code level="fatal" range=":-1"/>
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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12 <!-- In case the return code has not been set propery check stderr too -->
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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13 <regex level="fatal" match="Error:" source="both" />
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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14 <regex level="fatal" match="Exception:" source="both" />
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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15 <regex level="fatal_oom" match="Can't calloc" source="both" />
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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16 </stdio>
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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17 <version_command><![CDATA[
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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18 velocyto --version
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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19 ]]></version_command>
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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20 <command>
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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21 <![CDATA[
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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22 #import re
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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23
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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24 #if str($main.do) == "run10x":
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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25 ## We need to reproduce cell ranger structure:
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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26 mkdir -p '$main.sample/outs/filtered_gene_bc_matrices/whatever/' &&
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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27 ln -s '${main.BAM}' '$main.sample/outs/possorted_genome_bam.bam' &&
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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28 ln -s '${main.barcodes}' '$main.sample/outs/filtered_gene_bc_matrices/whatever/barcodes.tsv' &&
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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29 #else if str($main.do) in ['run', 'run-smartseq2']:
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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30 #for $bam in $main.bamfiles:
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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31 #set input_name = re.sub('[^\w\-\s]', '_', str($bam.element_identifier))
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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32 cp '$bam' '${input_name}.bam' &&
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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33 #end for
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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34 #end if
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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35 velocyto
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36
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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37 #if str($main.do) == "run":
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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38 run
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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39 @LOOMOUT@
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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40 #if str($main.b) != 'None':
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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41 -b '$main.b'
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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42 #end if
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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43 #if str($main.m) != 'None':
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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44 -m '$main.m'
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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45 #end if
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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46 $main.c
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47 $main.U
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48 #if str($main.u):
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49 -u '$main.u'
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50 #end if
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51 $main.M
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52 -t '$main.t'
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53 @SAMTOOLS_OPTS@
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54 $verbosity
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55 *.bam
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56 '$main.gtffile'
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57
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58 #else if str($main.do) == "run10x":
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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59 run10x
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60 #if str($main.s) != 'None':
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61 -s '$main.s'
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62 #end if
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63 #if str($main.m) != 'None':
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64 -m '$main.m'
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65 #end if
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66 $main.M
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67 -t '$main.t'
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68 @SAMTOOLS_OPTS@
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69 '$verbosity'
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70 '$main.sample'
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71 '$main.gtffile'
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72 && mv '$main.sample/velocyto/'*.loom 'output.loom'
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73
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74 #else if str($main.do) == "run-smartseq2":
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75 run-smartseq2
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76 @LOOMOUT@
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77 #if str($main.m) != 'None':
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78 -m '$main.m'
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79 #end if
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80 -t '$main.t'
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81 @SAMTOOLS_OPTS@
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82 '$verbosity'
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83 *.bam
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84 '$main.gtffile'
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85
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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86 #else if str($main.do) == "run-dropest":
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87 run-dropest
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88 @LOOMOUT@
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89 #if str($main.b) != 'None':
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90 -b '$main.b'
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91 #end if
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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92 #if str($main.m) != 'None':
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93 -m '$main.m'
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94 #end if
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95 -t '$main.t'
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96 @SAMTOOLS_OPTS@
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97 '$verbosity'
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98 '$main.bamfile'
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99 '$main.gtffile'
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100
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101 #else if str($main.do) == "dropest-bc-correct":
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102 tools dropest-bc-correct
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103 -o '$barcodesout'
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104 '$main.bamfile'
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105 '$main.rfile'
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106 #end if
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107
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108 ]]>
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109 </command>
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110 <inputs>
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111 <conditional name="main" >
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112 <param name="do" type="select" label="Pipeline"
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113 help="" >
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114 <option value="run10x" selected="true">Analysis for a 10x Chromium Sample</option>
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115 <option value="run-smartseq2">Analysis on SmartSeq2 data (BAM file per cell)</option>
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116 <option value="run-dropest">Analysis on DropEst preprocessed data</option>
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117 <!-- the above are wrappers for the main "run" command -->
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118 <option value="run" >Analysis for other protocols</option>
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119 <option value="dropest-bc-correct">Correct DropEst barcodes and produce valid barcodes file</option>
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120 </param>
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121 <when value="run10x" >
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122 <param name="sample" type="text" value="sample" label="sample name" help="This name will appear as prefix of each cell barcode.">
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123 <sanitizer invalid_char="">
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124 <valid initial="string.letters,string.digits">
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125 <add value="_" />
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126 </valid>
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127 </sanitizer>
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128 <validator type="regex">[0-9a-zA-Z_]+</validator>
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129 </param>
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130 <param name="BAM" type="data" format="bam" label="BAM file including CB tag" help="Can be Cell ranger output or STAR solo output" />
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131 <param name="barcodes" type="data" format="tsv,tabular,txt" label="List of valid cell barcodes" help="Can be STAR solo barcodes output" />
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132 <param name="gtffile" type="data" format="gtf" label="GTF file" />
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133 <param argument="-s" type="data" format="csv" optional="true"
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134 label="Metadata Table"
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135 help="Table containing metadata of the various samples (csv formatted rows are samples and cols are entries)" />
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136 <expand macro="repmask" />
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137 <expand macro="notuniquemappings" />
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138 <expand macro="loomdtype" token_16_selected="true" token_32_selected="false" />
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139 </when>
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140 <when value="run-smartseq2" >
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141 <param name="bamfiles" type="data" format="bam" multiple="true"
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142 label="BAM files" help="A BAM file for each cell. At least two required." />
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143 <param name="gtffile" type="data" format="gtf" label="GTF file" />
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144 <expand macro="repmask" />
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145 <expand macro="loomdtype" token_16_selected="false" token_32_selected="true" />
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146 </when>
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147 <when value="run-dropest" >
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148 <param name="bamfile" type="data" format="bam" label="BAM file" help="BAM file" />
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149 <param name="gtffile" type="data" format="gtf" label="GTF file" />
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150 <expand macro="bcffile" />
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151 <expand macro="repmask" />
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152 <expand macro="loomdtype" token_16_selected="false" token_32_selected="true" />
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153 </when>
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154 <when value="run" >
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155 <param name="bamfiles" type="data" format="bam" label="BAM file" help="BAM file" multiple="true"/>
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156 <param name="gtffile" type="data" format="gtf" label="GTF file" />
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157 <expand macro="bcffile" />
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158 <expand macro="repmask" />
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159 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
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160 label="One file per cell?"
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161 help="If this flag is used every bamfile passed is interpreted as an independent cell, otherwise multiple files are interpreted as batch of different cells to be analyzed together. Important: cells reads should not be distributed over multiple bamfiles is not supported!! (default: off)" />
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162 <param argument="-U" type="boolean" truevalue="-U" falsevalue="" checked="false"
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163 label="Without UMI?"
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164 help="If this flag is used the data is assumed UMI-less and reads are counted instead of molecules (default: off)" />
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165 <param argument="-u" type="text" value="" optional="true"
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166 label="UMI extension"
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167 help="In case UMI is too short to guarantee uniqueness (without information from the ampping) set this parameter to chr, Gene ro [N]bp If set to chr the mapping position (binned to 10Gb intervals) will be appended to UB (ideal for InDrops+dropEst). If set to Gene then the GX tag will be appended to the UB tag. If set to [N]bp the first N bases of the sequence will be used to extend UB (ideal for STRT). (Default: no)" />
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168 <expand macro="notuniquemappings" />
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169 <expand macro="loomdtype" token_16_selected="false" token_32_selected="true" />
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170 </when>
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171 <when value="dropest-bc-correct" >
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172 <param name="bamfile" type="data" format="BAM"
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173 label="Bam file with sorted reads obtained from DropEst" />
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174 <param name="rfile" type="data" format="rds"
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175 label="R dump RDS file generated from DropEst" />
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176 </when>
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177 </conditional>
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178 <param name="verbosity" type="select" label="verbosity level">
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179 <option value="-v">show only warning</option>
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180 <option value="-vv" selected="true">show warning and info</option>
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181 <option value="-vvv">show warning, info and debug</option>
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182 </param>
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183 </inputs>
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184 <outputs>
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185 <data format="loom" name="samples" from_work_dir="output.loom"/>
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186 <data name="barcodesout" format="txt" label="${tool.name} on ${on_string}: Barcodes file" >
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187 <filter>main['do']=='dropest-bc-correct'</filter>
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188 </data>
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189 </outputs>
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190 <tests>
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191 <!-- Test 1 10x -->
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192 <test expect_num_outputs="1">
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193 <conditional name="main">
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194 <param name="do" value="run10x"/>
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195 <param name="sample" value="sample"/>
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196 <param name="BAM" value="STARsolo_allSAMat.bam"/>
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197 <param name="barcodes" value="barcodes.tsv"/>
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198 <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
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199 <param name="M" value="false"/>
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200 <param name="t" value="uint16"/>
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201 </conditional>
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202 <output name="samples">
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203 <assert_contents>
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204 <has_size value="25996" delta="3000"/>
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205 </assert_contents>
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206 <metadata name="row_attrs_count" value="6" />
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207 <metadata name="layers_count" value="3" />
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208 <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
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209 <metadata name="col_attrs_count" value="1" />
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210 <metadata name="col_attrs_names" value="CellID" />
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211 </output>
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212 <assert_stdout>
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213 <has_text text="Counting for batch 1, containing 6 cells and 10 reads"/>
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214 </assert_stdout>
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215 </test>
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216 <!-- Test 2 run single bam as single cell -->
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217 <test expect_num_outputs="1">
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218 <conditional name="main">
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219 <param name="do" value="run"/>
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220 <param name="bamfiles" value="STARsolo_allSAMat.bam"/>
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221 <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
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222 <param name="c" value="true"/>
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223 <param name="U" value="true"/>
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224 <param name="M" value="false"/>
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225 <param name="t" value="uint16"/>
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226 </conditional>
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227 <output name="samples">
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228 <assert_contents>
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229 <has_size value="25927" delta="3000"/>
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230 </assert_contents>
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231 <metadata name="row_attrs_count" value="6" />
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232 <metadata name="layers_count" value="3" />
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233 <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
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234 <metadata name="col_attrs_count" value="1" />
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235 <metadata name="col_attrs_names" value="CellID" />
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236 </output>
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237 <assert_stdout>
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238 <has_text text="Counting for batch 1, containing 1 cells and 716 reads"/>
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239 </assert_stdout>
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240 </test>
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241 <!-- Test 3 run single bam as single cell with 2 bam -->
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242 <test expect_num_outputs="1">
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243 <conditional name="main">
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244 <param name="do" value="run"/>
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245 <param name="bamfiles" value="STARsolo_allSAMat.bam,STARsolo_allSAMat_copy.bam"/>
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246 <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
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247 <param name="c" value="true"/>
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248 <param name="U" value="true"/>
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249 <param name="M" value="false"/>
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250 <param name="t" value="uint16"/>
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251 </conditional>
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252 <output name="samples">
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253 <assert_contents>
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254 <has_size value="26384" delta="3000"/>
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255 </assert_contents>
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256 <metadata name="row_attrs_count" value="6" />
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257 <metadata name="layers_count" value="3" />
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258 <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
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259 <metadata name="col_attrs_count" value="1" />
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260 <metadata name="col_attrs_names" value="CellID" />
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261 </output>
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262 <assert_stdout>
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263 <has_text text="Counting for batch 2, containing 1 cells and 716 reads"/>
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264 </assert_stdout>
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265 </test>
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266 </tests>
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267 <help><![CDATA[
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268 Requirements on the input files
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269
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270 velocyto assumes that the bam file that is passed to the CLI contains a set of information and that some upstream analysis was performed on them already. In particular the bam file will have to:
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271
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272 Be sorted by mapping position.
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273 Represents either a single sample (multiple cells prepared using a certain barcode set in a single experiment) or single cell.
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274 Contain an error corrected cell barcodes as a TAG named CB or XC.
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275 Contain an error corrected molecular barcodes as a TAG named UB or XM.
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276
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277 Note
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278
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279 For SmartSeq2 bam files (3) and (4) are not required because it consists of one bam file per cell and no umi are present.
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280
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281 velocyto assumes that the gtf file follows the GENCODE gtf format description. However some mandatory field are relaxed to extend compatibility to a wider set of gtf files. In particular the gtf file will have to:
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282
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283 Contain the 3rd column entry feature-type. Note that only the exon entry of the gtf file marked as exon in this column will be considered and therefore the requirements below only apply to the ``exon`` labeled lines.
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284 Contain, in the 9th column, the key-value pair transcript_id, containing an unique identified for the transcript model.
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285 Contain, in the 9th column, the key-value pair transcript_name (Optional, if not present it will be set to the value of transcript_id)
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286 Contain, in the 9th column, the key-value pair gene_id, containing an unique identified for the gene.
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287 Contain, in the 9th column, the key-value pair gene_name (Optional, if not present it will be set to the value of gene_id)
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288 Contain, in the 9th column, the key-value pair exon_number (Recommended but optional, if not provided velocyto will sort exons in memory and number them)
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289
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290 ]]>
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291 </help>
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292 <expand macro="citations"/>
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293 </tool>