Mercurial > repos > iuc > umi_tools_count

annotate umi-tools_counts.xml @ 14:4f44381e2135 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 11a7415c7f8a44a3f990080533c1de43a41d1e2e
author iuc
date Fri, 28 Feb 2025 20:38:38 +0000
parents 4f81fcb5d271
children
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1 <tool id="umi_tools_count" name="UMI-tools count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>performs quantification of UMIs from BAM files</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 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
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10 @LINK_SAM_BAM_INPUT@
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11
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12 umi_tools count
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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13 '$wide_format_cell_counts'
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14 @BARCODE_OPTIONS@
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15 @UMI_GROUPING_OPTIONS@
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16 @SC_OPTIONS@
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17 @SAMBAM_OPTIONS@
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18 @ADVANCED_OPTIONS@
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19 -I '$input_file' -S '$out_counts'
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20 @LOG@
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21 #if str($cond_extra.prepender) != "none":
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22 #if str($cond_extra.prepender) == "string":
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23 #set $replacer = str($cond_extra.custom_label)
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24 #else
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25 #set $replacer = re.sub('[^\w\_]+', '_', str($input.element_identifier.rsplit('.',1)[0]))
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26 #end if
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27 && sed -i -r '1s|\b([ACGT]+)\b|'"$replacer"'_\1|g' '$out_counts'
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28 #end if
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29 ]]></command>
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30 <inputs>
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31 <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" />
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32 <param 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" />
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33 <expand macro="barcode_options_macro"/>
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34 <expand macro="umi_grouping_options_macro"/>
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35 <expand macro="sambam_options_macro"/>
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36 <expand macro="sc_options_macro"/>
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37 <expand macro="advanced_options_macro"/>
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38 <conditional name="cond_extra" >
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39 <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" >
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40 <option value="none" selected="true" >No modifications</option>
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41 <option value="string">Custom Label</option>
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42 <option value="dataset name">Dataset Name</option>
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43 </param>
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44 <when value="none"></when>
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45 <when value="dataset name"></when>
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46 <when value="string">
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47 <param name="custom_label" type="text" label="Label to Prepend" >
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48 <sanitizer invalid_char="">
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49 <valid initial="string.letters,string.digits">
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50 <add value="-"/>
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51 <add value="_"/>
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52 <add value="."/>
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53 </valid>
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54 </sanitizer>
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55 </param>
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56 </when>
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57 </conditional>
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58 <expand macro="log_input_macro"/>
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59 </inputs>
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60 <outputs>
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61 <data name="out_counts" format="tabular" />
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62 <expand macro="log_output_macro"/>
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63 </outputs>
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64 <tests>
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65 <test expect_num_outputs="1"><!--count_single_gene_tag:-->
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66 <param name="input" value="chr19_gene_tags.bam" />
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67 <section name="advanced">
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68 <param name="random_seed" value="123456789" />
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69 </section>
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70 <section name="sc">
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71 <param name="gene_tag" value="XF" />
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72 <param name="skip_tags_regex" value="^[__|Unassigned]" />
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73 <param name="per_cell" value="false" />
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74 </section>
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75 <conditional name="bc">
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76 <param name="extract_umi_method" value="umis" />
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77 </conditional>
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78 <section name="umi">
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79 <param name="method" value="directional" />
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80 </section>
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81 <param name="wide_format_cell_counts" value="false" />
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82 <output name="out_counts" value="count_single_gene_tag.tsv" />
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83 </test>
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84 <test expect_num_outputs="1"><!--count_single_gene_tag .. with sam input-->
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85 <param name="input" value="chr19_gene_tags.sam" />
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86 <section name="advanced">
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87 <param name="random_seed" value="123456789" />
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88 </section>
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89 <section name="sc">
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90 <param name="gene_tag" value="XF" />
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diff changeset
91 <param name="skip_tags_regex" value="^[__|Unassigned]" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
92 <param name="per_cell" value="false" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
93 </section>
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
94 <conditional name="bc">
733b904db6bb "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="extract_umi_method" value="umis" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
96 </conditional>
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
97 <section name="umi">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
98 <param name="method" value="directional" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
99 </section>
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
100 <param name="wide_format_cell_counts" value="false" />
0
1a893fb3ab98 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
101 <output name="out_counts" value="count_single_gene_tag.tsv" />
1a893fb3ab98 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
102 </test>
12
4f81fcb5d271 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a
iuc
parents: 8
diff changeset
103 <test expect_num_outputs="1"><!--count_single_cells_gene_tag:-->
8
733b904db6bb "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="input" value="chr19_gene_tags.bam" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
105 <section name="advanced">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
106 <param name="random_seed" value="123456789" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
107 </section>
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
108 <section name="sc">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
109 <param name="gene_tag" value="XF" />
733b904db6bb "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="skip_tags_regex" value="^[__|Unassigned]" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
111 <param name="per_cell" value="true" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
112 </section>
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
113 <conditional name="bc">
733b904db6bb "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="extract_umi_method" value="umis" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
115 </conditional>
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
116 <section name="umi">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
117 <param name="method" value="directional" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
118 </section>
1
807eb1f05add planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a
iuc
parents: 0
diff changeset
119 <param name="wide_format_cell_counts" value="false" />
0
1a893fb3ab98 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
120 <output name="out_counts" value="count_single_cells_gene_tag.tsv" />
1a893fb3ab98 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
121 </test>
12
4f81fcb5d271 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a
iuc
parents: 8
diff changeset
122 <test expect_num_outputs="1"><!--count_single_cells_wide_gene_tag:-->
8
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
123 <param name="input" value="chr19_gene_tags.bam" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
124 <section name="advanced">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
125 <param name="random_seed" value="123456789" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
126 </section>
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
127 <section name="sc">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
128 <param name="gene_tag" value="XF" />
733b904db6bb "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="skip_tags_regex" value="^[__|Unassigned]" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
130 <param name="per_cell" value="true" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
131 </section>
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
132 <conditional name="bc">
733b904db6bb "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="extract_umi_method" value="umis" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
134 </conditional>
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
135 <section name="umi">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
136 <param name="method" value="directional" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
137 </section>
0
1a893fb3ab98 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
138 <param name="wide_format_cell_counts" value="true" />
1a893fb3ab98 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
139 <output name="out_counts" value="count_single_cells_gene_tag_wide.tsv" />
1a893fb3ab98 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
iuc
parents:
diff changeset
140 </test>
12
4f81fcb5d271 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a
iuc
parents: 8
diff changeset
141 <test expect_num_outputs="1"><!-- count ENSDARG00000019692, with defaults -->
8
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
142 <param name="input" value="fc.ENSDARG00000019692.bam" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
143 <section name="advanced">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
144 <param name="random_seed" value="0" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
145 </section>
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
146 <section name="sc">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
147 <param name="gene_tag" value="XT" />
733b904db6bb "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="per_cell" value="true" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
149 </section>
733b904db6bb "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="umi">
733b904db6bb "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="method" value="unique" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
152 </section>
1
807eb1f05add planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a
iuc
parents: 0
diff changeset
153 <output name="out_counts" value="fc.ENSDARG00000019692.counts" />
807eb1f05add planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a
iuc
parents: 0
diff changeset
154 </test>
12
4f81fcb5d271 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a
iuc
parents: 8
diff changeset
155 <test expect_num_outputs="1"><!-- count ENSDARG00000019692, relabel string -->
8
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
156 <param name="input" value="fc.ENSDARG00000019692.bam" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
157 <section name="advanced">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
158 <param name="random_seed" value="0" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
159 </section>
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
160 <section name="sc">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
161 <param name="gene_tag" value="XT" />
733b904db6bb "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="per_cell" value="true" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
163 </section>
733b904db6bb "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="umi">
733b904db6bb "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="method" value="unique" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
166 </section>
3
199dfadab14d planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
167 <conditional name="cond_extra" >
199dfadab14d planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
168 <param name="prepender" value="string" />
199dfadab14d planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
169 <param name="custom_label" value="test" />
199dfadab14d planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
170 </conditional>
199dfadab14d planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
171 <output name="out_counts" value="fc.ENSDARG00000019692.counts.test" />
199dfadab14d planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
iuc
parents: 1
diff changeset
172 </test>
12
4f81fcb5d271 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a
iuc
parents: 8
diff changeset
173 <test expect_num_outputs="1"><!-- count ENSDARG00000019692, relabel filename -->
8
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
174 <param name="input" value="fc.ENSDARG00000019692.bam" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
175 <section name="advanced">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
176 <param name="random_seed" value="0" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
177 </section>
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
178 <section name="sc">
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
diff changeset
179 <param name="gene_tag" value="XT" />
733b904db6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 6
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180 <param name="per_cell" value="true" />
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181 </section>
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182 <section name="umi">
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183 <param name="method" value="unique" />
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184 </section>
3
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185 <conditional name="cond_extra" >
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186 <param name="prepender" value="dataset name" />
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187 </conditional>
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188 <output name="out_counts" value="fc.ENSDARG00000019692.counts.name" />
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189 </test>
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190 </tests>
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191 <help><![CDATA[
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192
8
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193 count - Count reads per gene from BAM using UMIs and mapping coordinates
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194 ========================================================================
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195
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196 This tool is only designed to work with library preparation
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197 methods where the fragmentation occurs after amplification, as per
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198 most single cell RNA-Seq methods (e.g 10x, inDrop, Drop-seq, SCRB-seq
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199 and CEL-seq2). Since the precise mapping co-ordinate is not longer
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200 informative for such library preparations, it is simplified to the
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201 gene. This is a reasonable approach providing the number of available
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202 UMIs is sufficiently high and the sequencing depth is sufficiently low
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203 that the probability of two reads from the same gene having the same
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204 UMIs is acceptably low.
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205
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206 If you want to count reads per gene for library preparations which
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207 fragment prior to amplification (e.g bulk RNA-Seq), please use
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208 ``umi_tools dedup`` to remove the duplicate reads as this will use the
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209 full information from the mapping co-ordinate. Then use a read
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210 counting tool such as FeatureCounts or HTSeq to count the reads per
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211 gene.
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212
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213 In the rare case of bulk RNA-Seq using a library preparation method
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214 with fragmentation after amplification, one can still use ``count`` but
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215 note that it has not been tested on bulk RNA-Seq.
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216
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217 This tool deviates from group and dedup in that the ``--per-gene`` option
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218 is hardcoded on.
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219
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220 @BARCODE_HELP@
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221
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222 @UMI_GROUPING_HELP@
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223
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224 ]]></help>
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225 <expand macro="citations" />
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226 </tool>