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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@VERSION@">0.1.0</token>
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4 <token name="@IDX_VERSION@">q1</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">kb-python</requirement>
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8 </requirements>
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9 </xml>
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10 <xml name="citations">
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11 <citations>
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12 <citation type="doi">add citation</citation>
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13 </citations>
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14 </xml>
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15 <xml name="index">
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16 <conditional name="refTranscriptSource">
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17 <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?">
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18 <option value="history">Use an index from your history</option>
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19 <option value="built" selected="True">Built one </option>
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20 </param>
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21 <when value="history">
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22 <section name="h_index" title="Select the index files from your history:" expanded="true">
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23 <param name="index_file" type="data" format="kallisto.idx" label="kb index file (.idx)"/>
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24 <param name="t2g_file" type="data" format="txt" label="Transcript to gene (t2g) file"/>
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25 <section name="history_lamanno" title="Additional index files" expanded="false">
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26 <param name="cdna_t2c" optional="true" type="data" format="txt" label="-c1 cDNA transcripts-to-captures (t2c) file (only needed with workflow==lamanno or nucleus)"/>
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27 <param name="intron_t2c" optional="true" type="data" format="txt" label="-c2 intron transcripts-to-captures (t2c) file (only needed with workflow==lamanno or nucleus)"/>
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28 </section>
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29 </section>
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30 </when>
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31 <when value="built">
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32 <section name="s_index" title="Kb index" expanded="true">
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33 <param name="genomic_fasta" type="data" optional="true" format="fasta" label="Genomic fasta file (leave empty when: workflow = kite)"/>
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34 <param name="genomic_gtf" type="data" optional="true" format="gtf" label="Genomic gtf file (leave empty when: workflow = kite)"/>
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35 <param name="kite_table" type="data" label="Kite table of feature barcodes and IDs (only required when workflow = kite)" optional="true" format="tabular"/>
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36 </section>
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37 </when>
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38 </conditional>
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39 </xml>
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40 <xml name="tests">
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41 <!-- Test1: Test with pre-built index provided by user -->
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42 <test>
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43 <conditional name="refTranscriptSource">
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44 <param name="TranscriptSource" value="history"/>
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45 <section name="h_index">
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46 <param name="index_file" value="GRCm39.gencode.chr19_sub.kb_ref.idx"/>
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47 <param name="t2g_file" value="GRCm39.gencode.chr19_sub.t2g.txt"/>
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48 </section>
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49 </conditional>
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50 <param name="technology" value="10XV2"/>
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51 <param name="workflow" value="standard"/>
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52 <param name="FASTQ1" value="SRR8599150_S1_L001_R1_001.100k_lines.fastq.gz"/>
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53 <param name="FASTQ2" value="SRR8599150_S1_L001_R2_001.100k_lines.fastq.gz"/>
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54 <param name="extra_dtype" value="none"/>
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55 <output name="barcodes" file="barcodes.tsv" compare="sim_size" delta="100000" ftype="txt"/>
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56 <output name="genes" file="genes.tsv" compare="sim_size" delta="100000" ftype="txt"/>
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57 <output name="matrix" file="matrix.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
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58 </test>
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59 <!--Test2: Test with building the index on the fly, before kb count.-->
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60 <test>
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61 <conditional name="refTranscriptSource">
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62 <param name="TranscriptSource" value="built"/>
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63 <section name="s_index">
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64 <param name="genomic_fasta" value="GRCm39.chr19_100k.fa.gz"/>
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65 <param name="genomic_gtf" value="gencode.VM26.chr19_10k.gtf.gz"/>
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66 </section>
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67 </conditional>
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68 <param name="technology" value="10XV2"/>
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69 <param name="workflow" value="standard"/>
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70 <param name="FASTQ1" value="SRR8599150_S1_L001_R1_001.100k_lines.fastq.gz"/>
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71 <param name="FASTQ2" value="SRR8599150_S1_L001_R2_001.100k_lines.fastq.gz"/>
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72 <param name="extra_dtype" value="none"/>
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73 <output name="barcodes" file="barcodes.tsv" compare="sim_size" delta="100000" ftype="txt"/>
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74 <output name="genes" file="genes.tsv" compare="sim_size" delta="100000" ftype="txt"/>
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75 <output name="matrix" file="matrix.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
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76 </test>
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77 <!--Test3: Test lamanno workflow with pre-built index.-->
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78 <test>
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79 <conditional name="refTranscriptSource">
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80 <param name="TranscriptSource" value="history"/>
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81 <section name="h_index">
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82 <param name="index_file" value="kb_ref.lamanno.idx"/>
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83 <param name="t2g_file" value="t2g.lamanno.txt"/>
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84 <section name="history_lamanno">
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85 <param name="cdna_t2c" value="cdna_t2c.lamanno.txt"/>
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86 <param name="intron_t2c" value="intron_t2c.lamanno.txt"/>
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87 </section>
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88 </section>
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89 </conditional>
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90 <param name="technology" value="10XV2"/>
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91 <param name="workflow" value="lamanno"/>
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92 <param name="FASTQ1" value="SRR8599150_S1_L001_R1_001.100k_lines.fastq.gz"/>
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93 <param name="FASTQ2" value="SRR8599150_S1_L001_R2_001.100k_lines.fastq.gz"/>
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94 <param name="extra_dtype" value="none"/>
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95 <output name="barcodes" file="barcodes.lamanno.tsv" compare="sim_size" delta="100000" ftype="txt"/>
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96 <output name="genes" file="genes.lamanno.tsv" compare="sim_size" delta="100000" ftype="txt"/>
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97 <output name="matrix" file="matrix.lamanno.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
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98 </test>
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99 <!--Test:4 Test lamanno workflow with building the index on the fly, before kb count.-->
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100 <test>
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101 <conditional name="refTranscriptSource">
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102 <param name="TranscriptSource" value="built"/>
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103 <section name="s_index">
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104 <param name="genomic_fasta" value="GRCm39.chr19_100k.fa.gz"/>
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105 <param name="genomic_gtf" value="gencode.VM26.chr19_10k.gtf.gz"/>
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106 </section>
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107 </conditional>
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108 <param name="technology" value="10XV2"/>
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109 <param name="workflow" value="lamanno"/>
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110 <param name="FASTQ1" value="SRR8599150_S1_L001_R1_001.100k_lines.fastq.gz"/>
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111 <param name="FASTQ2" value="SRR8599150_S1_L001_R2_001.100k_lines.fastq.gz"/>
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112 <param name="extra_dtype" value="none"/>
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113 <output name="barcodes" file="barcodes.lamanno.tsv" compare="sim_size" delta="100000" ftype="txt"/>
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114 <output name="genes" file="genes.lamanno.tsv" compare="sim_size" delta="100000" ftype="txt"/>
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115 <output name="matrix" file="matrix.lamanno.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
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116 </test>
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117 <!--Test:5 Test kite workflow with pre-built index.-->
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118 <test>
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119 <conditional name="refTranscriptSource">
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120 <param name="TranscriptSource" value="history"/>
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121 <section name="h_index">
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122 <param name="index_file" value="mismatch.idx"/>
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123 <param name="t2g_file" value="t2g.kite.txt"/>
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124 </section>
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125 </conditional>
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126 <param name="technology" value="10XV3"/>
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127 <param name="workflow" value="kite"/>
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128 <param name="FASTQ1" value="pbmc_1k_protein_v3_antibody_S2_L001_R1_001.100k_sub.fastq.gz"/>
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129 <param name="FASTQ2" value="pbmc_1k_protein_v3_antibody_S2_L001_R2_001.100k_sub.fastq.gz"/>
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130 <param name="extra_dtype" value="none"/>
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131 <output name="barcodes" file="barcodes.kite.tsv" compare="sim_size" delta="100000" ftype="txt"/>
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132 <output name="genes" file="genes.kite.tsv" compare="sim_size" delta="100000" ftype="txt"/>
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133 <output name="matrix" file="matrix.kite.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
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134 </test>
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135 <!--Test:6 Test kite workflow with building the index on the fly, before kb count.-->
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136 <test>
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137 <conditional name="refTranscriptSource">
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138 <param name="TranscriptSource" value="built"/>
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139 <section name="s_index">
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140 <param name="kite_table" value="kite_features.tsv"/>
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141 </section>
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142 </conditional>
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143 <param name="technology" value="10XV3"/>
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144 <param name="workflow" value="kite"/>
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145 <param name="FASTQ1" value="pbmc_1k_protein_v3_antibody_S2_L001_R1_001.100k_sub.fastq.gz"/>
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146 <param name="FASTQ2" value="pbmc_1k_protein_v3_antibody_S2_L001_R2_001.100k_sub.fastq.gz"/>
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147 <param name="extra_dtype" value="none"/>
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148 <output name="barcodes" file="barcodes.kite.tsv" compare="sim_size" delta="100000" ftype="txt"/>
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149 <output name="genes" file="genes.kite.tsv" compare="sim_size" delta="100000" ftype="txt"/>
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150 <output name="matrix" file="matrix.kite.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
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151 </test>
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152 </xml>
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153 </macros>
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