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1 <tool id="kb_python" name="kb_python" version="@VERSION@+galaxy1">
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2 <description>performs gene and feature quantification on single-cell sequencing data.</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 <requirements>
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7 <requirement type="package" version="@VERSION@" >kb-python</requirement>
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8 <requirement type="package" version="1.0.0">jupyter</requirement>
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9 </requirements>
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10
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11 <stdio>
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12 <exit_code range="1:" />
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13 <exit_code range=":-1" />
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14 <regex match="Error:" />
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15 <regex match="Exception:" />
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16 <regex match="Exception :" />
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17 </stdio>
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18 <command detect_errors="exit_code"><![CDATA[
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19 mkdir ./index
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20 && mkdir ./kb_outs
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21 #if $refTranscriptSource.TranscriptSource == "history":
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22 && ln -s '${refTranscriptSource.h_index.index_file}' './index/kb_ref.idx'
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23 && ln -s '${refTranscriptSource.h_index.t2g_file}' './index/t2g.txt'
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24 #if $workflow == "lamanno" or $workflow == "nucleus":
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25 && ln -s '${refTranscriptSource.h_index.history_lamanno.cdna_t2c}' './index/cdna_t2c.txt'
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26 && ln -s '${refTranscriptSource.h_index.history_lamanno.intron_t2c}' './index/intron_t2c.txt'
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27 #end if
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28 #set $index_path = './index'
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29 #else if $refTranscriptSource.TranscriptSource == "built":
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30 && kb ref -i ./index/kb_ref.idx
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31 -g ./index/t2g.txt
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32 -f1 ./index/cdna.fa
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33 --workflow $workflow
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34 #if $workflow == "lamanno" or $workflow == "nucleus":
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35 -f2 ./index/intron.fa
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36 -c1 ./index/cdna_t2c.txt
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37 -c2 ./index/intron_t2c.txt
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38 --workflow $workflow
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39 #end if
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40 #if $workflow != "kite":
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41 '${refTranscriptSource.s_index.genomic_fasta}'
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42 '${refTranscriptSource.s_index.genomic_gtf}'
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43 #else:
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44 '${refTranscriptSource.s_index.kite_table}'
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45 #end if
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46 #set $index_path = './index'
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47 #end if
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48 && kb count
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49 -t \${GALAXY_SLOTS:-1}
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50 -i $index_path/kb_ref.idx
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51 -g $index_path/t2g.txt
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52 #if $workflow == "lamanno" or $workflow == "nucleus":
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53 -c1 $index_path/cdna_t2c.txt
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54 -c2 $index_path/intron_t2c.txt
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55 #end if
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56 -x $technology
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57 #if $whitelist:
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58 --whitelist '${optional.whitelist}'
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59 #end if
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60 ${optional.multimap}
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61 ${optional.report}
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62 --workflow $workflow
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63 #if $extra_dtype != "none":
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64 $extra_dtype
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65 #end if
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66 -o ./kb_outs
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67 --cellranger
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68 $FASTQ1
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69 $FASTQ2
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70 ]]>
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71 </command>
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72 <inputs>
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73 <param name="workflow" label="Select the workflow you want to use:" type="select" multiple="false" format="text" help="Type of workflow. Use `lamanno` for RNA velocity based on La Manno et al. 2018 logic.
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74 Use `nucleus` for RNA velocity on single-nucleus RNA-seq reads. Use `kite` for feature barcoding. Use `kite:10xFB` for 10x Genomics Feature Barcoding technology.">
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75 <option value="standard">standard</option>
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76 <option value="lamanno">lamanno</option>
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77 <option value="nucleus">nucleus</option>
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78 <option value="kite">kite</option>
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79 </param>
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80 <expand macro="index"/>
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81 <param name="technology" label="Select the scRNA-seq technology:" type="select" multiple="false" format="text" help="Choose the scRNA-seq technology used to generate the fastq data.">
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82 <option value="10XV1">10XV1</option>
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83 <option value="10XV2">10XV2</option>
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84 <option value="10XV3">10XV3</option>
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85 <option value="CELSEQ">CELSEQ</option>
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86 <option value="CELSEQ2">CELSEQ2</option>
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87 <option value="DROPSEQ">DROPSEQ</option>
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88 <option value="INDROPSV1">INDROPSV1</option>
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89 <option value="INDROPSV2">INDROPSV2</option>
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90 <option value="INDROPSV3">INDROPSV3</option>
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91 <option value="SCRUBSEQ">SCRUBSEQ</option>
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92 <option value="SURECELL">SURECELL</option>
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93 </param>
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94 <param name="FASTQ1" label="Select the R1 fastq file:" type="data" format="fastqsanger.gz" multiple="false"/>
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95 <param name="FASTQ2" label="Select the R2 fastq file:" type="data" format="fastqsanger.gz" multiple="false"/>
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96 <param name="extra_dtype" type="select" label="Do you want any additional output data type beside CellRanger?">
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97 <option value="none" selected = "true">No</option>
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98 <option value="--loom">Loom</option>
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99 <option value="--h5ad">H5ad</option>
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100 </param>
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101 <section name="optional" title="Optional commands" expanded="false">
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102 <param name="whitelist" type="data" format="tsv,tabular" optional="true" label="Whitelist file" help="Whitelisted barcodes to correct to. If not provided and bustools supports the technology, a pre-packaged whitelist is used. If not, the bustools
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103 whitelist command is used."/>
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104 <param name="multimap" type="boolean" optional="true" truevalue="--mm" falsevalue="" label="Include multi pseudoaligned reads?" help="Do you want to include reads that pseudoalign to multiple genes?"/>
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105 <param name="report" type="boolean" optional="true" truevalue="--report" falsevalue="" label="Create an html report?" help="If true, will create an html report with mapping statistics and cell" checked="false"/>
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106 </section>
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107 </inputs>
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108 <outputs>
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109 <data name="barcodes" label="cellranger barcodes" format="txt" from_work_dir="kb_outs/counts_unfiltered/cellranger/barcodes.tsv"/>
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110 <data name="genes" label="cellranger genes" format="txt" from_work_dir="kb_outs/counts_unfiltered/cellranger/genes.tsv"/>
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111 <data name="matrix" label="cellranger matrix" format="mtx" from_work_dir="kb_outs/counts_unfiltered/cellranger/matrix.mtx" />
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112 <data name="inspect" label="inspect_report" format="json" from_work_dir="kb_outs/inspect.json"/>
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113 <data name="runinfo" label="run info" format="json" from_work_dir="kb_outs/run_info.json"/>
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114 <data name="kbinfo" label="kb info" format="json" from_work_dir="kb_outs/kb_info.json"/>
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115 <data name="kb_ref" label="kb_ref.idx" format="kallisto.idx" from_work_dir="index/kb_ref.idx">
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116 <filter>refTranscriptSource['TranscriptSource'] == "built"</filter>
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117 </data>
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118 <data name="t2g" label="t2g.txt" format="txt" from_work_dir="index/t2g.txt">
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119 <filter>refTranscriptSource['TranscriptSource'] == "built"</filter>
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120 </data>
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121 <data name="cdna_t2c" label="-c1 cdna_t2c.txt" format="txt" from_work_dir="index/cdna_t2c.txt">
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122 <filter>refTranscriptSource['TranscriptSource'] == "built"</filter>
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123 <filter>workflow == "lamanno"</filter>
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124 </data>
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125 <data name="intron_t2c" label="-c2 intron_t2c.txt" format="txt" from_work_dir="index/intron_t2c.txt">
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126 <filter>refTranscriptSource['TranscriptSource'] == "built"</filter>
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127 <filter>workflow == "lamanno"</filter>
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128 </data>
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129 <data name="adata" label="adata.h5ad" format="h5ad" from_work_dir="kb_outs/counts_unfiltered/adata.h5ad">
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130 <filter >extra_dtype == "--h5ad"</filter>
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131 </data>
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132 <data name="adata" label="adata.loom" format="loom" from_work_dir="kb_outs/counts_unfiltered/adata.loom">
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133 <filter>extra_dtype == "--loom"</filter>
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134 </data>
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135 <data name="report" label="report.html" format="html" from_work_dir="kb_outs/report.html">
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136 <filter>optional["report"]</filter>
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137 </data>
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138 </outputs>
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139 <tests>
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140 <expand macro="tests"/>
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141 </tests>
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142 <help><![CDATA[
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143 This is a galaxy wrapper for kallisto-bustools (kb) for quantification of different types of single-cell sequencing data. The main kallisto-bustools homepage can be found under:
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144 'kallisto-bustools<https://www.kallistobus.tools/>'.
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145
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146 The kb count command runs the kallisto and bustools programs. It can be used for pre-processing of data from a variety of single-cell RNA-seq technologies,
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147 and for a number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.).
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148
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149 The kb package is developed and maintained by the Pachterlab under the MIT License.
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150 ]]></help>
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151 <citations>
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152 <citation type="doi">https://doi.org/10.1101/673285</citation>
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153 </citations>
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154 </tool> |
