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comparison umi-tools_counts.xml @ 12:71ad4a56c40c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a
author iuc
date Sat, 05 Oct 2024 13:08:27 +0000
parents e654095ab143
children
comparison
equal deleted inserted replaced
11:9570563fb686 12:71ad4a56c40c
1 <tool id="umi_tools_count" name="UMI-tools count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="umi_tools_count" name="UMI-tools count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>performs quantification of UMIs from BAM files</description> 2 <description>performs quantification of UMIs from BAM files</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <!-- TODO see comment in LINK_SAM_BAM_INPUT --> 8 <!-- TODO see comment in LINK_SAM_BAM_INPUT -->
9 <requirement type="package" version="1.12">samtools</requirement> 9 <requirement type="package" version="1.12">samtools</requirement>
10 <requirement type="package" version="4.7">sed</requirement> 10 <requirement type="package" version="4.7">sed</requirement>
11 </expand> 11 </expand>
31 && sed -i -r '1s|\b([ACGT]+)\b|'"$replacer"'_\1|g' '$out_counts' 31 && sed -i -r '1s|\b([ACGT]+)\b|'"$replacer"'_\1|g' '$out_counts'
32 #end if 32 #end if
33 ]]></command> 33 ]]></command>
34 <inputs> 34 <inputs>
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" /> 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" />
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" /> 36 <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" />
37 <expand macro="barcode_options_macro"/> 37 <expand macro="barcode_options_macro"/>
38 <expand macro="umi_grouping_options_macro"/> 38 <expand macro="umi_grouping_options_macro"/>
39 <expand macro="sambam_options_macro"/> 39 <expand macro="sambam_options_macro"/>
40 <expand macro="sc_options_macro"/> 40 <expand macro="sc_options_macro"/>
41 <expand macro="advanced_options_macro"/> 41 <expand macro="advanced_options_macro"/>
64 <outputs> 64 <outputs>
65 <data name="out_counts" format="tabular" /> 65 <data name="out_counts" format="tabular" />
66 <expand macro="log_output_macro"/> 66 <expand macro="log_output_macro"/>
67 </outputs> 67 </outputs>
68 <tests> 68 <tests>
69 <test><!--count_single_gene_tag:--> 69 <test expect_num_outputs="1"><!--count_single_gene_tag:-->
70 <param name="input" value="chr19_gene_tags.bam" /> 70 <param name="input" value="chr19_gene_tags.bam" />
71 <section name="advanced"> 71 <section name="advanced">
72 <param name="random_seed" value="123456789" /> 72 <param name="random_seed" value="123456789" />
73 </section> 73 </section>
74 <section name="sc"> 74 <section name="sc">
83 <param name="method" value="directional" /> 83 <param name="method" value="directional" />
84 </section> 84 </section>
85 <param name="wide_format_cell_counts" value="false" /> 85 <param name="wide_format_cell_counts" value="false" />
86 <output name="out_counts" value="count_single_gene_tag.tsv" /> 86 <output name="out_counts" value="count_single_gene_tag.tsv" />
87 </test> 87 </test>
88 <test><!--count_single_gene_tag .. with sam input--> 88 <test expect_num_outputs="1"><!--count_single_gene_tag .. with sam input-->
89 <param name="input" value="chr19_gene_tags.sam" /> 89 <param name="input" value="chr19_gene_tags.sam" />
90 <section name="advanced"> 90 <section name="advanced">
91 <param name="random_seed" value="123456789" /> 91 <param name="random_seed" value="123456789" />
92 </section> 92 </section>
93 <section name="sc"> 93 <section name="sc">
102 <param name="method" value="directional" /> 102 <param name="method" value="directional" />
103 </section> 103 </section>
104 <param name="wide_format_cell_counts" value="false" /> 104 <param name="wide_format_cell_counts" value="false" />
105 <output name="out_counts" value="count_single_gene_tag.tsv" /> 105 <output name="out_counts" value="count_single_gene_tag.tsv" />
106 </test> 106 </test>
107 <test><!--count_single_cells_gene_tag:--> 107 <test expect_num_outputs="1"><!--count_single_cells_gene_tag:-->
108 <param name="input" value="chr19_gene_tags.bam" /> 108 <param name="input" value="chr19_gene_tags.bam" />
109 <section name="advanced"> 109 <section name="advanced">
110 <param name="random_seed" value="123456789" /> 110 <param name="random_seed" value="123456789" />
111 </section> 111 </section>
112 <section name="sc"> 112 <section name="sc">
121 <param name="method" value="directional" /> 121 <param name="method" value="directional" />
122 </section> 122 </section>
123 <param name="wide_format_cell_counts" value="false" /> 123 <param name="wide_format_cell_counts" value="false" />
124 <output name="out_counts" value="count_single_cells_gene_tag.tsv" /> 124 <output name="out_counts" value="count_single_cells_gene_tag.tsv" />
125 </test> 125 </test>
126 <test><!--count_single_cells_wide_gene_tag:--> 126 <test expect_num_outputs="1"><!--count_single_cells_wide_gene_tag:-->
127 <param name="input" value="chr19_gene_tags.bam" /> 127 <param name="input" value="chr19_gene_tags.bam" />
128 <section name="advanced"> 128 <section name="advanced">
129 <param name="random_seed" value="123456789" /> 129 <param name="random_seed" value="123456789" />
130 </section> 130 </section>
131 <section name="sc"> 131 <section name="sc">
140 <param name="method" value="directional" /> 140 <param name="method" value="directional" />
141 </section> 141 </section>
142 <param name="wide_format_cell_counts" value="true" /> 142 <param name="wide_format_cell_counts" value="true" />
143 <output name="out_counts" value="count_single_cells_gene_tag_wide.tsv" /> 143 <output name="out_counts" value="count_single_cells_gene_tag_wide.tsv" />
144 </test> 144 </test>
145 <test><!-- count ENSDARG00000019692, with defaults --> 145 <test expect_num_outputs="1"><!-- count ENSDARG00000019692, with defaults -->
146 <param name="input" value="fc.ENSDARG00000019692.bam" /> 146 <param name="input" value="fc.ENSDARG00000019692.bam" />
147 <section name="advanced"> 147 <section name="advanced">
148 <param name="random_seed" value="0" /> 148 <param name="random_seed" value="0" />
149 </section> 149 </section>
150 <section name="sc"> 150 <section name="sc">
154 <section name="umi"> 154 <section name="umi">
155 <param name="method" value="unique" /> 155 <param name="method" value="unique" />
156 </section> 156 </section>
157 <output name="out_counts" value="fc.ENSDARG00000019692.counts" /> 157 <output name="out_counts" value="fc.ENSDARG00000019692.counts" />
158 </test> 158 </test>
159 <test><!-- count ENSDARG00000019692, relabel string --> 159 <test expect_num_outputs="1"><!-- count ENSDARG00000019692, relabel string -->
160 <param name="input" value="fc.ENSDARG00000019692.bam" /> 160 <param name="input" value="fc.ENSDARG00000019692.bam" />
161 <section name="advanced"> 161 <section name="advanced">
162 <param name="random_seed" value="0" /> 162 <param name="random_seed" value="0" />
163 </section> 163 </section>
164 <section name="sc"> 164 <section name="sc">
172 <param name="prepender" value="string" /> 172 <param name="prepender" value="string" />
173 <param name="custom_label" value="test" /> 173 <param name="custom_label" value="test" />
174 </conditional> 174 </conditional>
175 <output name="out_counts" value="fc.ENSDARG00000019692.counts.test" /> 175 <output name="out_counts" value="fc.ENSDARG00000019692.counts.test" />
176 </test> 176 </test>
177 <test><!-- count ENSDARG00000019692, relabel filename --> 177 <test expect_num_outputs="1"><!-- count ENSDARG00000019692, relabel filename -->
178 <param name="input" value="fc.ENSDARG00000019692.bam" /> 178 <param name="input" value="fc.ENSDARG00000019692.bam" />
179 <section name="advanced"> 179 <section name="advanced">
180 <param name="random_seed" value="0" /> 180 <param name="random_seed" value="0" />
181 </section> 181 </section>
182 <section name="sc"> 182 <section name="sc">