Mercurial > repos > iuc > velocyto_cli

annotate velocyto_cli.xml @ 1:4a75f9c84a4b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9
author iuc
date Mon, 15 May 2023 10:03:25 +0000
parents 81ad264c1548
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
4a75f9c84a4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9
iuc
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1 <tool id="velocyto_cli" name="velocyto CLI" version="@VERSION@+galaxy1">
0
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
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3 <macros>
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4 <import>macros.xml</import>
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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"/>
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7 <expand macro="requirements"/>
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8 <stdio>
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9 <!-- Anything other than zero is an error -->
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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
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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>
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17 <version_command><![CDATA[
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18 velocyto --version
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19 ]]></version_command>
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20 <command>
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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
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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($main.do) == "run10x":
1
4a75f9c84a4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9
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25 #if str($main.sample_definition.sample_definition_select) == "manual":
4a75f9c84a4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9
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26 #set sample = str($main.sample_definition.sample)
4a75f9c84a4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9
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27 #else:
4a75f9c84a4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9
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28 #set sample = re.sub('[^\w\-\s]', '_', str($main.BAM.element_identifier))
4a75f9c84a4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9
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29 #end if
0
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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30 ## We need to reproduce cell ranger structure:
1
4a75f9c84a4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9
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31 mkdir -p '$sample/outs/filtered_gene_bc_matrices/whatever/' &&
4a75f9c84a4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9
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32 ln -s '${main.BAM}' '$sample/outs/possorted_genome_bam.bam' &&
4a75f9c84a4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9
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33 ln -s '${main.barcodes}' '$sample/outs/filtered_gene_bc_matrices/whatever/barcodes.tsv' &&
0
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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34 #else if str($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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35 #for $bam in $main.bamfiles:
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36 #set input_name = re.sub('[^\w\-\s]', '_', str($bam.element_identifier))
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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37 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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38 #end for
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39 #end if
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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40 velocyto
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41
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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42 #if str($main.do) == "run":
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43 run
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44 @LOOMOUT@
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45 #if str($main.b) != 'None':
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46 -b '$main.b'
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47 #end if
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48 #if str($main.m) != 'None':
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49 -m '$main.m'
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50 #end if
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51 $main.c
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52 $main.U
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53 #if str($main.u):
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54 -u '$main.u'
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55 #end if
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56 $main.M
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57 -t '$main.t'
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58 @SAMTOOLS_OPTS@
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59 $verbosity
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60 *.bam
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61 '$main.gtffile'
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62
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63 #else if str($main.do) == "run10x":
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64 run10x
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65 #if str($main.s) != 'None':
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66 -s '$main.s'
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67 #end if
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68 #if str($main.m) != 'None':
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69 -m '$main.m'
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70 #end if
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71 $main.M
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72 -t '$main.t'
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73 @SAMTOOLS_OPTS@
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74 '$verbosity'
1
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75 '$sample'
0
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76 '$main.gtffile'
1
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77 && mv '$sample/velocyto/'*.loom 'output.loom'
0
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78
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79 #else if str($main.do) == "run-smartseq2":
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80 run-smartseq2
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81 @LOOMOUT@
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82 #if str($main.m) != 'None':
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83 -m '$main.m'
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84 #end if
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85 -t '$main.t'
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86 @SAMTOOLS_OPTS@
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87 '$verbosity'
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88 *.bam
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89 '$main.gtffile'
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90
81ad264c1548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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91 #else if str($main.do) == "run-dropest":
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92 run-dropest
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93 @LOOMOUT@
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94 #if str($main.b) != 'None':
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95 -b '$main.b'
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96 #end if
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97 #if str($main.m) != 'None':
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98 -m '$main.m'
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99 #end if
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100 -t '$main.t'
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101 @SAMTOOLS_OPTS@
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102 '$verbosity'
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103 '$main.bamfile'
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104 '$main.gtffile'
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105
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106 #else if str($main.do) == "dropest-bc-correct":
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107 tools dropest-bc-correct
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108 -o '$barcodesout'
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109 '$main.bamfile'
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110 '$main.rfile'
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111 #end if
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112
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113 ]]>
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114 </command>
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115 <inputs>
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116 <conditional name="main" >
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117 <param name="do" type="select" label="Pipeline"
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118 help="" >
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119 <option value="run10x" selected="true">Analysis for a 10x Chromium Sample</option>
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120 <option value="run-smartseq2">Analysis on SmartSeq2 data (BAM file per cell)</option>
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121 <option value="run-dropest">Analysis on DropEst preprocessed data</option>
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122 <!-- the above are wrappers for the main "run" command -->
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123 <option value="run" >Analysis for other protocols</option>
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124 <option value="dropest-bc-correct">Correct DropEst barcodes and produce valid barcodes file</option>
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125 </param>
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126 <when value="run10x" >
1
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127 <conditional name="sample_definition">
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128 <param name="sample_definition_select" type="select" label="How to set sample name" help="This name will appear as prefix of each cell barcode.">
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129 <option value="manual">Manually</option>
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130 <option value="identifier">Automatic (use identifier in history)</option>
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131 </param>
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132 <when value="manual">
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133 <param name="sample" type="text" value="sample" label="sample name" help="">
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134 <sanitizer invalid_char="">
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135 <valid initial="string.letters,string.digits">
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136 <add value="_" />
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137 </valid>
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138 </sanitizer>
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139 <validator type="regex">[0-9a-zA-Z_]+</validator>
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140 </param>
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141 </when>
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142 <when value="identifier"/>
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143 </conditional>
0
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144 <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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145 <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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146 <param name="gtffile" type="data" format="gtf" label="GTF file" />
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147 <param argument="-s" type="data" format="csv" optional="true"
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148 label="Metadata Table"
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149 help="Table containing metadata of the various samples (csv formatted rows are samples and cols are entries)" />
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150 <expand macro="repmask" />
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151 <expand macro="notuniquemappings" />
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152 <expand macro="loomdtype" token_16_selected="true" token_32_selected="false" />
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153 </when>
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154 <when value="run-smartseq2" >
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155 <param name="bamfiles" type="data" format="bam" multiple="true"
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156 label="BAM files" help="A BAM file for each cell. At least two required." />
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157 <param name="gtffile" type="data" format="gtf" label="GTF file" />
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158 <expand macro="repmask" />
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159 <expand macro="loomdtype" token_16_selected="false" token_32_selected="true" />
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160 </when>
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161 <when value="run-dropest" >
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162 <param name="bamfile" type="data" format="bam" label="BAM file" help="BAM file" />
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163 <param name="gtffile" type="data" format="gtf" label="GTF file" />
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164 <expand macro="bcffile" />
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165 <expand macro="repmask" />
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166 <expand macro="loomdtype" token_16_selected="false" token_32_selected="true" />
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167 </when>
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168 <when value="run" >
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169 <param name="bamfiles" type="data" format="bam" label="BAM file" help="BAM file" multiple="true"/>
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170 <param name="gtffile" type="data" format="gtf" label="GTF file" />
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171 <expand macro="bcffile" />
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172 <expand macro="repmask" />
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173 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
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174 label="One file per cell?"
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175 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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176 <param argument="-U" type="boolean" truevalue="-U" falsevalue="" checked="false"
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177 label="Without UMI?"
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178 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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179 <param argument="-u" type="text" value="" optional="true"
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180 label="UMI extension"
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181 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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182 <expand macro="notuniquemappings" />
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183 <expand macro="loomdtype" token_16_selected="false" token_32_selected="true" />
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184 </when>
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185 <when value="dropest-bc-correct" >
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186 <param name="bamfile" type="data" format="BAM"
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187 label="Bam file with sorted reads obtained from DropEst" />
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188 <param name="rfile" type="data" format="rds"
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189 label="R dump RDS file generated from DropEst" />
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190 </when>
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191 </conditional>
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192 <param name="verbosity" type="select" label="verbosity level">
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193 <option value="-v">show only warning</option>
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194 <option value="-vv" selected="true">show warning and info</option>
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195 <option value="-vvv">show warning, info and debug</option>
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196 </param>
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197 </inputs>
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198 <outputs>
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199 <data format="loom" name="samples" from_work_dir="output.loom"/>
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200 <data name="barcodesout" format="txt" label="${tool.name} on ${on_string}: Barcodes file" >
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201 <filter>main['do']=='dropest-bc-correct'</filter>
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202 </data>
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203 </outputs>
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204 <tests>
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205 <!-- Test 1 10x -->
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206 <test expect_num_outputs="1">
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207 <conditional name="main">
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208 <param name="do" value="run10x"/>
1
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209 <conditional name="sample_definition">
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210 <param name="sample_definition_select" value="manual"/>
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211 <param name="sample" value="sample"/>
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212 </conditional>
0
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213 <param name="BAM" value="STARsolo_allSAMat.bam"/>
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214 <param name="barcodes" value="barcodes.tsv"/>
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215 <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
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216 <param name="M" value="false"/>
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217 <param name="t" value="uint16"/>
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218 </conditional>
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219 <output name="samples">
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220 <assert_contents>
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221 <has_size value="25996" delta="3000"/>
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222 </assert_contents>
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223 <metadata name="row_attrs_count" value="6" />
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224 <metadata name="layers_count" value="3" />
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225 <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
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226 <metadata name="col_attrs_count" value="1" />
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227 <metadata name="col_attrs_names" value="CellID" />
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228 </output>
1
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229 <assert_command>
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230 <has_text text="sample"/>
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231 </assert_command>
0
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232 <assert_stdout>
1
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233 <has_text text="Counting for batch 1, containing 6 cells and 10 reads"/>
0
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234 </assert_stdout>
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235 </test>
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236 <!-- Test 2 run single bam as single cell -->
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237 <test expect_num_outputs="1">
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238 <conditional name="main">
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239 <param name="do" value="run"/>
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240 <param name="bamfiles" value="STARsolo_allSAMat.bam"/>
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241 <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
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242 <param name="c" value="true"/>
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243 <param name="U" value="true"/>
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244 <param name="M" value="false"/>
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245 <param name="t" value="uint16"/>
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246 </conditional>
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247 <output name="samples">
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248 <assert_contents>
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249 <has_size value="25927" delta="3000"/>
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250 </assert_contents>
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251 <metadata name="row_attrs_count" value="6" />
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252 <metadata name="layers_count" value="3" />
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253 <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
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254 <metadata name="col_attrs_count" value="1" />
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255 <metadata name="col_attrs_names" value="CellID" />
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256 </output>
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257 <assert_stdout>
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258 <has_text text="Counting for batch 1, containing 1 cells and 716 reads"/>
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259 </assert_stdout>
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260 </test>
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261 <!-- Test 3 run single bam as single cell with 2 bam -->
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262 <test expect_num_outputs="1">
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263 <conditional name="main">
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264 <param name="do" value="run"/>
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265 <param name="bamfiles" value="STARsolo_allSAMat.bam,STARsolo_allSAMat_copy.bam"/>
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266 <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
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267 <param name="c" value="true"/>
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268 <param name="U" value="true"/>
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269 <param name="M" value="false"/>
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270 <param name="t" value="uint16"/>
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271 </conditional>
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272 <output name="samples">
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273 <assert_contents>
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274 <has_size value="26384" delta="3000"/>
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275 </assert_contents>
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276 <metadata name="row_attrs_count" value="6" />
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277 <metadata name="layers_count" value="3" />
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278 <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
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279 <metadata name="col_attrs_count" value="1" />
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280 <metadata name="col_attrs_names" value="CellID" />
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281 </output>
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282 <assert_stdout>
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283 <has_text text="Counting for batch 2, containing 1 cells and 716 reads"/>
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284 </assert_stdout>
1
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285 </test>
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286 <!-- Test 4 10x indentifyer -->
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287 <test expect_num_outputs="1">
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288 <conditional name="main">
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289 <param name="do" value="run10x"/>
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290 <conditional name="sample_definition">
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291 <param name="sample_definition_select" value="identifier"/>
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292 </conditional>
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293 <param name="BAM" value="STARsolo_allSAMat.bam"/>
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294 <param name="barcodes" value="barcodes.tsv"/>
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295 <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
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296 <param name="M" value="false"/>
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297 <param name="t" value="uint16"/>
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298 </conditional>
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299 <output name="samples">
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300 <assert_contents>
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301 <has_size value="25996" delta="3000"/>
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302 </assert_contents>
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303 <metadata name="row_attrs_count" value="6" />
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304 <metadata name="layers_count" value="3" />
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305 <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
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306 <metadata name="col_attrs_count" value="1" />
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307 <metadata name="col_attrs_names" value="CellID" />
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308 </output>
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309 <assert_command>
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310 <has_text text="STARsolo_allSAMat"/>
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311 <not_has_text text="sample"/>
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312 </assert_command>
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313 <assert_stdout>
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314 <has_text text="Counting for batch 1, containing 6 cells and 10 reads"/>
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315 </assert_stdout>
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316 </test>
0
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317 </tests>
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318 <help><![CDATA[
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319 Requirements on the input files
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320
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321 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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322
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323 Be sorted by mapping position.
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324 Represents either a single sample (multiple cells prepared using a certain barcode set in a single experiment) or single cell.
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325 Contain an error corrected cell barcodes as a TAG named CB or XC.
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326 Contain an error corrected molecular barcodes as a TAG named UB or XM.
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327
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328 Note
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329
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330 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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331
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332 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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333
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334 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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335 Contain, in the 9th column, the key-value pair transcript_id, containing an unique identified for the transcript model.
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336 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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337 Contain, in the 9th column, the key-value pair gene_id, containing an unique identified for the gene.
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338 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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339 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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340
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341 ]]>
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342 </help>
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343 <expand macro="citations"/>
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344 </tool>