Mercurial > repos > iuc > umi_tools_count

annotate umi-tools_counts.xml @ 8:e654095ab143 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
author iuc
date Mon, 13 Sep 2021 14:49:44 +0000
parents 276b4111b253
children 71ad4a56c40c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
1 <tool id="umi_tools_count" name="UMI-tools count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1
3c932ad4a174 planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a
iuc
parents: 0
diff changeset
2 <description>performs quantification of UMIs from BAM files</description>
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
3 <expand macro="bio_tools"/>
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
4 <macros>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
5 <import>macros.xml</import>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
6 </macros>
6
276b4111b253 "planemo upload commit 6ba769440f8f6a62e9ebfac069a30edc541bac0a"
iuc
parents: 5
diff changeset
7 <expand macro="requirements">
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
8 <!-- TODO see comment in LINK_SAM_BAM_INPUT -->
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
9 <requirement type="package" version="1.12">samtools</requirement>
6
276b4111b253 "planemo upload commit 6ba769440f8f6a62e9ebfac069a30edc541bac0a"
iuc
parents: 5
diff changeset
10 <requirement type="package" version="4.7">sed</requirement>
276b4111b253 "planemo upload commit 6ba769440f8f6a62e9ebfac069a30edc541bac0a"
iuc
parents: 5
diff changeset
11 </expand>
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
13 #import re
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
14 @LINK_SAM_BAM_INPUT@
1
3c932ad4a174 planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a
iuc
parents: 0
diff changeset
15
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
16 umi_tools count
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
17 '$wide_format_cell_counts'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
18 @BARCODE_OPTIONS@
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
19 @UMI_GROUPING_OPTIONS@
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
20 @SC_OPTIONS@
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
21 @SAMBAM_OPTIONS@
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
22 @ADVANCED_OPTIONS@
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
23 -I '$input_file' -S '$out_counts'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
24 @LOG@
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
25 #if str($cond_extra.prepender) != "none":
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
26 #if str($cond_extra.prepender) == "string":
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
27 #set $replacer = str($cond_extra.custom_label)
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
28 #else
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
29 #set $replacer = re.sub('[^\w\_]+', '_', str($input.element_identifier.rsplit('.',1)[0]))
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
30 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
31 && sed -i -r '1s|\b([ACGT]+)\b|'"$replacer"'_\1|g' '$out_counts'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
32 #end if
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
33 ]]></command>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
34 <inputs>
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
35 <param name="input" type="data" format="sam,bam" label="Reads to deduplicate in SAM or BAM format" help="Please use the samtools sort tool to ensure a correct BAM input" />
1
3c932ad4a174 planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a
iuc
parents: 0
diff changeset
36 <param argument="--wide-format-cell-counts" name="wide_format_cell_counts" type="boolean" truevalue="--wide-format-cell-counts" falsevalue="" checked="true" label="Output a matrix of genes and cells, instead of a flat file" />
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
37 <expand macro="barcode_options_macro"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
38 <expand macro="umi_grouping_options_macro"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
39 <expand macro="sambam_options_macro"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
40 <expand macro="sc_options_macro"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
41 <expand macro="advanced_options_macro"/>
3
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
42 <conditional name="cond_extra" >
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
43 <param name="prepender" type="select" label="Prepend a label to all column headers" help="This preserves uniqueness when merging with other files with the same headers. Note: filename must not contain a '.' character" >
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
44 <option value="none" selected="true" >No modifications</option>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
45 <option value="string">Custom Label</option>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
46 <option value="dataset name">Dataset Name</option>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
47 </param>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
48 <when value="none"></when>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
49 <when value="dataset name"></when>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
50 <when value="string">
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
51 <param name="custom_label" type="text" label="Label to Prepend" >
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
52 <sanitizer invalid_char="">
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
53 <valid initial="string.letters,string.digits">
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
54 <add value="-"/>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
55 <add value="_"/>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
56 <add value="."/>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
57 </valid>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
58 </sanitizer>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
59 </param>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
60 </when>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
61 </conditional>
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
62 <expand macro="log_input_macro"/>
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
63 </inputs>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
64 <outputs>
1
3c932ad4a174 planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a
iuc
parents: 0
diff changeset
65 <data name="out_counts" format="tabular" />
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
66 <expand macro="log_output_macro"/>
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
67 </outputs>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
68 <tests>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
69 <test><!--count_single_gene_tag:-->
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
70 <param name="input" value="chr19_gene_tags.bam" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
71 <section name="advanced">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
72 <param name="random_seed" value="123456789" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
73 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
74 <section name="sc">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
75 <param name="gene_tag" value="XF" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
76 <param name="skip_tags_regex" value="^[__|Unassigned]" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
77 <param name="per_cell" value="false" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
78 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
79 <conditional name="bc">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
80 <param name="extract_umi_method" value="umis" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
81 </conditional>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
82 <section name="umi">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
83 <param name="method" value="directional" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
84 </section>
1
3c932ad4a174 planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a
iuc
parents: 0
diff changeset
85 <param name="wide_format_cell_counts" value="false" />
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
86 <output name="out_counts" value="count_single_gene_tag.tsv" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
87 </test>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
88 <test><!--count_single_gene_tag .. with sam input-->
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
89 <param name="input" value="chr19_gene_tags.sam" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
90 <section name="advanced">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
91 <param name="random_seed" value="123456789" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
92 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
93 <section name="sc">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
94 <param name="gene_tag" value="XF" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
95 <param name="skip_tags_regex" value="^[__|Unassigned]" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
96 <param name="per_cell" value="false" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
97 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
98 <conditional name="bc">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
99 <param name="extract_umi_method" value="umis" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
100 </conditional>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
101 <section name="umi">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
102 <param name="method" value="directional" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
103 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
104 <param name="wide_format_cell_counts" value="false" />
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
105 <output name="out_counts" value="count_single_gene_tag.tsv" />
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
106 </test>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
107 <test><!--count_single_cells_gene_tag:-->
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
108 <param name="input" value="chr19_gene_tags.bam" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
109 <section name="advanced">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
110 <param name="random_seed" value="123456789" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
111 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
112 <section name="sc">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
113 <param name="gene_tag" value="XF" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
114 <param name="skip_tags_regex" value="^[__|Unassigned]" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
115 <param name="per_cell" value="true" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
116 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
117 <conditional name="bc">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
118 <param name="extract_umi_method" value="umis" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
119 </conditional>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
120 <section name="umi">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
121 <param name="method" value="directional" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
122 </section>
1
3c932ad4a174 planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a
iuc
parents: 0
diff changeset
123 <param name="wide_format_cell_counts" value="false" />
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
124 <output name="out_counts" value="count_single_cells_gene_tag.tsv" />
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
125 </test>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
126 <test><!--count_single_cells_wide_gene_tag:-->
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
127 <param name="input" value="chr19_gene_tags.bam" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
128 <section name="advanced">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
129 <param name="random_seed" value="123456789" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
130 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
131 <section name="sc">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
132 <param name="gene_tag" value="XF" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
133 <param name="skip_tags_regex" value="^[__|Unassigned]" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
134 <param name="per_cell" value="true" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
135 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
136 <conditional name="bc">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
137 <param name="extract_umi_method" value="umis" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
138 </conditional>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
139 <section name="umi">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
140 <param name="method" value="directional" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
141 </section>
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
142 <param name="wide_format_cell_counts" value="true" />
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
143 <output name="out_counts" value="count_single_cells_gene_tag_wide.tsv" />
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
144 </test>
1
3c932ad4a174 planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a
iuc
parents: 0
diff changeset
145 <test><!-- count ENSDARG00000019692, with defaults -->
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
146 <param name="input" value="fc.ENSDARG00000019692.bam" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
147 <section name="advanced">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
148 <param name="random_seed" value="0" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
149 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
150 <section name="sc">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
151 <param name="gene_tag" value="XT" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
152 <param name="per_cell" value="true" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
153 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
154 <section name="umi">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
155 <param name="method" value="unique" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
156 </section>
1
3c932ad4a174 planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a
iuc
parents: 0
diff changeset
157 <output name="out_counts" value="fc.ENSDARG00000019692.counts" />
3c932ad4a174 planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a
iuc
parents: 0
diff changeset
158 </test>
3
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
159 <test><!-- count ENSDARG00000019692, relabel string -->
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
160 <param name="input" value="fc.ENSDARG00000019692.bam" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
161 <section name="advanced">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
162 <param name="random_seed" value="0" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
163 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
164 <section name="sc">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
165 <param name="gene_tag" value="XT" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
166 <param name="per_cell" value="true" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
167 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
168 <section name="umi">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
169 <param name="method" value="unique" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
170 </section>
3
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
171 <conditional name="cond_extra" >
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
172 <param name="prepender" value="string" />
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
173 <param name="custom_label" value="test" />
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
174 </conditional>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
175 <output name="out_counts" value="fc.ENSDARG00000019692.counts.test" />
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
176 </test>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
177 <test><!-- count ENSDARG00000019692, relabel filename -->
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
178 <param name="input" value="fc.ENSDARG00000019692.bam" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
179 <section name="advanced">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
180 <param name="random_seed" value="0" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
181 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
182 <section name="sc">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
183 <param name="gene_tag" value="XT" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
184 <param name="per_cell" value="true" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
185 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
186 <section name="umi">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
187 <param name="method" value="unique" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
188 </section>
3
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
189 <conditional name="cond_extra" >
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
190 <param name="prepender" value="dataset name" />
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
191 </conditional>
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
192 <output name="out_counts" value="fc.ENSDARG00000019692.counts.name" />
b557acca0b56 planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
193 </test>
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
194 </tests>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
195 <help><![CDATA[
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
196
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
197 count - Count reads per gene from BAM using UMIs and mapping coordinates
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
198 ========================================================================
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
199
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
200 This tool is only designed to work with library preparation
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
201 methods where the fragmentation occurs after amplification, as per
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
202 most single cell RNA-Seq methods (e.g 10x, inDrop, Drop-seq, SCRB-seq
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
203 and CEL-seq2). Since the precise mapping co-ordinate is not longer
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
204 informative for such library preparations, it is simplified to the
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
205 gene. This is a reasonable approach providing the number of available
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
206 UMIs is sufficiently high and the sequencing depth is sufficiently low
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
207 that the probability of two reads from the same gene having the same
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
208 UMIs is acceptably low.
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
209
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
210 If you want to count reads per gene for library preparations which
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
211 fragment prior to amplification (e.g bulk RNA-Seq), please use
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
212 ``umi_tools dedup`` to remove the duplicate reads as this will use the
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
213 full information from the mapping co-ordinate. Then use a read
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
214 counting tool such as FeatureCounts or HTSeq to count the reads per
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
215 gene.
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
216
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
217 In the rare case of bulk RNA-Seq using a library preparation method
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
218 with fragmentation after amplification, one can still use ``count`` but
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
219 note that it has not been tested on bulk RNA-Seq.
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
220
8
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
221 This tool deviates from group and dedup in that the ``--per-gene`` option
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
222 is hardcoded on.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
223
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
224 @BARCODE_HELP@
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
225
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
226 @UMI_GROUPING_HELP@
0
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
227
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
228 ]]></help>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
229 <expand macro="citations" />
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
230 </tool>