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comparison genap2_kb_python/macros.xml @ 0:e8d93f1429c2 draft

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author fwuennemann
date Fri, 16 Apr 2021 18:18:21 +0000
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-1:000000000000 0:e8d93f1429c2
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@VERSION@">0.1.0</token>
4 <token name="@IDX_VERSION@">q1</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@VERSION@">kb-python</requirement>
8 </requirements>
9 </xml>
10 <xml name="citations">
11 <citations>
12 <citation type="doi">add citation</citation>
13 </citations>
14 </xml>
15 <xml name="index">
16 <conditional name="refTranscriptSource">
17 <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?">
18 <option value="history">Use an index from your history</option>
19 <option value="built" selected="True">Built one </option>
20 </param>
21 <when value="history">
22 <section name="h_index" title="Select the index files from your history:" expanded="true">
23 <param name="index_file" type="data" format="kallisto.idx" label="kb index file (.idx)"/>
24 <param name="t2g_file" type="data" format="txt" label="Transcript to gene (t2g) file"/>
25 <section name="history_lamanno" title="Additional index files" expanded="false">
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)"/>
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)"/>
28 </section>
29 </section>
30 </when>
31 <when value="built">
32 <section name="s_index" title="Kb index" expanded="true">
33 <param name="genomic_fasta" type="data" optional="true" format="fasta" label="Genomic fasta file (leave empty when: workflow = kite)"/>
34 <param name="genomic_gtf" type="data" optional="true" format="gtf" label="Genomic gtf file (leave empty when: workflow = kite)"/>
35 <param name="kite_table" type="data" label="Kite table of feature barcodes and IDs (only required when workflow = kite)" optional="true" format="tabular"/>
36 </section>
37 </when>
38 </conditional>
39 </xml>
40 <xml name="tests">
41 <!-- Test1: Test with pre-built index provided by user -->
42 <test>
43 <conditional name="refTranscriptSource">
44 <param name="TranscriptSource" value="history"/>
45 <section name="h_index">
46 <param name="index_file" value="GRCm39.gencode.chr19_sub.kb_ref.idx"/>
47 <param name="t2g_file" value="GRCm39.gencode.chr19_sub.t2g.txt"/>
48 </section>
49 </conditional>
50 <param name="technology" value="10XV2"/>
51 <param name="workflow" value="standard"/>
52 <param name="FASTQ1" value="SRR8599150_S1_L001_R1_001.100k_lines.fastq.gz"/>
53 <param name="FASTQ2" value="SRR8599150_S1_L001_R2_001.100k_lines.fastq.gz"/>
54 <param name="extra_dtype" value="none"/>
55 <output name="barcodes" file="barcodes.tsv" compare="sim_size" delta="100000" ftype="txt"/>
56 <output name="genes" file="genes.tsv" compare="sim_size" delta="100000" ftype="txt"/>
57 <output name="matrix" file="matrix.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
58 </test>
59 <!--Test2: Test with building the index on the fly, before kb count.-->
60 <test>
61 <conditional name="refTranscriptSource">
62 <param name="TranscriptSource" value="built"/>
63 <section name="s_index">
64 <param name="genomic_fasta" value="GRCm39.chr19_100k.fa.gz"/>
65 <param name="genomic_gtf" value="gencode.VM26.chr19_10k.gtf.gz"/>
66 </section>
67 </conditional>
68 <param name="technology" value="10XV2"/>
69 <param name="workflow" value="standard"/>
70 <param name="FASTQ1" value="SRR8599150_S1_L001_R1_001.100k_lines.fastq.gz"/>
71 <param name="FASTQ2" value="SRR8599150_S1_L001_R2_001.100k_lines.fastq.gz"/>
72 <param name="extra_dtype" value="none"/>
73 <output name="barcodes" file="barcodes.tsv" compare="sim_size" delta="100000" ftype="txt"/>
74 <output name="genes" file="genes.tsv" compare="sim_size" delta="100000" ftype="txt"/>
75 <output name="matrix" file="matrix.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
76 </test>
77 <!--Test3: Test lamanno workflow with pre-built index.-->
78 <test>
79 <conditional name="refTranscriptSource">
80 <param name="TranscriptSource" value="history"/>
81 <section name="h_index">
82 <param name="index_file" value="kb_ref.lamanno.idx"/>
83 <param name="t2g_file" value="t2g.lamanno.txt"/>
84 <section name="history_lamanno">
85 <param name="cdna_t2c" value="cdna_t2c.lamanno.txt"/>
86 <param name="intron_t2c" value="intron_t2c.lamanno.txt"/>
87 </section>
88 </section>
89 </conditional>
90 <param name="technology" value="10XV2"/>
91 <param name="workflow" value="lamanno"/>
92 <param name="FASTQ1" value="SRR8599150_S1_L001_R1_001.100k_lines.fastq.gz"/>
93 <param name="FASTQ2" value="SRR8599150_S1_L001_R2_001.100k_lines.fastq.gz"/>
94 <param name="extra_dtype" value="none"/>
95 <output name="barcodes" file="barcodes.lamanno.tsv" compare="sim_size" delta="100000" ftype="txt"/>
96 <output name="genes" file="genes.lamanno.tsv" compare="sim_size" delta="100000" ftype="txt"/>
97 <output name="matrix" file="matrix.lamanno.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
98 </test>
99 <!--Test:4 Test lamanno workflow with building the index on the fly, before kb count.-->
100 <test>
101 <conditional name="refTranscriptSource">
102 <param name="TranscriptSource" value="built"/>
103 <section name="s_index">
104 <param name="genomic_fasta" value="GRCm39.chr19_100k.fa.gz"/>
105 <param name="genomic_gtf" value="gencode.VM26.chr19_10k.gtf.gz"/>
106 </section>
107 </conditional>
108 <param name="technology" value="10XV2"/>
109 <param name="workflow" value="lamanno"/>
110 <param name="FASTQ1" value="SRR8599150_S1_L001_R1_001.100k_lines.fastq.gz"/>
111 <param name="FASTQ2" value="SRR8599150_S1_L001_R2_001.100k_lines.fastq.gz"/>
112 <param name="extra_dtype" value="none"/>
113 <output name="barcodes" file="barcodes.lamanno.tsv" compare="sim_size" delta="100000" ftype="txt"/>
114 <output name="genes" file="genes.lamanno.tsv" compare="sim_size" delta="100000" ftype="txt"/>
115 <output name="matrix" file="matrix.lamanno.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
116 </test>
117 <!--Test:5 Test kite workflow with pre-built index.-->
118 <test>
119 <conditional name="refTranscriptSource">
120 <param name="TranscriptSource" value="history"/>
121 <section name="h_index">
122 <param name="index_file" value="mismatch.idx"/>
123 <param name="t2g_file" value="t2g.kite.txt"/>
124 </section>
125 </conditional>
126 <param name="technology" value="10XV3"/>
127 <param name="workflow" value="kite"/>
128 <param name="FASTQ1" value="pbmc_1k_protein_v3_antibody_S2_L001_R1_001.100k_sub.fastq.gz"/>
129 <param name="FASTQ2" value="pbmc_1k_protein_v3_antibody_S2_L001_R2_001.100k_sub.fastq.gz"/>
130 <param name="extra_dtype" value="none"/>
131 <output name="barcodes" file="barcodes.kite.tsv" compare="sim_size" delta="100000" ftype="txt"/>
132 <output name="genes" file="genes.kite.tsv" compare="sim_size" delta="100000" ftype="txt"/>
133 <output name="matrix" file="matrix.kite.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
134 </test>
135 <!--Test:6 Test kite workflow with building the index on the fly, before kb count.-->
136 <test>
137 <conditional name="refTranscriptSource">
138 <param name="TranscriptSource" value="built"/>
139 <section name="s_index">
140 <param name="kite_table" value="kite_features.tsv"/>
141 </section>
142 </conditional>
143 <param name="technology" value="10XV3"/>
144 <param name="workflow" value="kite"/>
145 <param name="FASTQ1" value="pbmc_1k_protein_v3_antibody_S2_L001_R1_001.100k_sub.fastq.gz"/>
146 <param name="FASTQ2" value="pbmc_1k_protein_v3_antibody_S2_L001_R2_001.100k_sub.fastq.gz"/>
147 <param name="extra_dtype" value="none"/>
148 <output name="barcodes" file="barcodes.kite.tsv" compare="sim_size" delta="100000" ftype="txt"/>
149 <output name="genes" file="genes.kite.tsv" compare="sim_size" delta="100000" ftype="txt"/>
150 <output name="matrix" file="matrix.kite.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
151 </test>
152 </xml>
153 </macros>