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comparison macros.xml @ 17:428735be9764 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 13:08:51 +0000
parents 257be15474a7
children
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equal deleted inserted replaced
16:257be15474a7 17:428735be9764
2 <macros> 2 <macros>
3 3
4 <!-- macros applying to all umi_tools --> 4 <!-- macros applying to all umi_tools -->
5 5
6 <token name="@TOOL_VERSION@">1.1.5</token> 6 <token name="@TOOL_VERSION@">1.1.5</token>
7 <token name="@VERSION_SUFFIX@">0</token> 7 <token name="@VERSION_SUFFIX@">1</token>
8 <token name="@PROFILE@">21.01</token> 8 <token name="@PROFILE@">23.1</token>
9 <xml name="requirements"> 9 <xml name="requirements">
10 <requirements> 10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">umi_tools</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">umi_tools</requirement>
12 <yield /> 12 <yield />
13 </requirements> 13 </requirements>
102 <when value="single"> 102 <when value="single">
103 <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" /> 103 <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
104 <expand macro="barcode1_macro"/> 104 <expand macro="barcode1_macro"/>
105 </when> 105 </when>
106 <when value="paired"> 106 <when value="paired">
107 <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" /> 107 <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Forward reads in FASTQ format" />
108 <param name="input_read2" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" /> 108 <param name="input_read2" type="data" format="@FASTQ_FORMATS@" label="Reverse reads in FASTQ format" />
109 <expand macro="barcode1_macro"/> 109 <expand macro="barcode1_macro"/>
110 <expand macro="barcode2_macro"/> 110 <expand macro="barcode2_macro"/>
111 <yield/> 111 <yield/>
112 </when> 112 </when>
113 <when value="paired_collection"> 113 <when value="paired_collection">
150 150
151 <!-- macros for count, dedup, and group --> 151 <!-- macros for count, dedup, and group -->
152 152
153 <token name="@LINK_SAM_BAM_INPUT@"><![CDATA[ 153 <token name="@LINK_SAM_BAM_INPUT@"><![CDATA[
154 #if $input.is_of_type("sam"): 154 #if $input.is_of_type("sam"):
155 ## TODO dedup has problems with SAM input in some cases 155 ## sam input is not supported for paired data
156 ## https://github.com/CGATOxford/UMI-tools/issues/483 156 ## https://github.com/CGATOxford/UMI-tools/issues/483
157 ## so convert it to sorted BAM for now 157 ## so convert it to sorted BAM
158 ## #set $input_file = $input 158 ## #set $input_file = $input
159 samtools sort --no-PG '$input' > 'input.bam' && 159 samtools sort --no-PG '$input' -O BAM > 'input.bam' &&
160 samtools index -b 'input.bam' && 160 samtools index -b 'input.bam' &&
161 #set $input_file = 'input.bam' 161 #set $input_file = 'input.bam'
162 #else: 162 #else:
163 ln -sf '${input}' 'input.bam' && 163 ln -sf '${input}' 'input.bam' &&
164 ln -sf '$input.metadata.bam_index' 'input.bam.bai' && 164 ln -sf '$input.metadata.bam_index' 'input.bam.bai' &&
165 #set $input_file = 'input.bam' 165 #set $input_file = 'input.bam'
166 #end if 166 #end if
167 ]]></token> 167 ]]></token>
168 <token name="@SET_INPUT_TYPE@"><![CDATA[ 168 <token name="@SET_INPUT_TYPE@"><![CDATA[
169 ## TODO see comment in LINK_SAM_BAM_INPUT 169 ## see comment in LINK_SAM_BAM_INPUT
170 ## #if $input.is_of_type("sam"): 170 ## #if $input.is_of_type("sam"):
171 ## --in-sam 171 ## --in-sam
172 ## #end if 172 ## #end if
173 ]]></token> 173 ]]></token>
174 174
509 <expand macro="sanitize_tag" /> 509 <expand macro="sanitize_tag" />
510 </param> 510 </param>
511 <param argument="--assigned-status-tag" type="text" optional="true" label="Bam tag describing whether read is assigned to a gene" help="By default, this is set as the same tag as --gene-tag"> 511 <param argument="--assigned-status-tag" type="text" optional="true" label="Bam tag describing whether read is assigned to a gene" help="By default, this is set as the same tag as --gene-tag">
512 <expand macro="sanitize_tag" /> 512 <expand macro="sanitize_tag" />
513 </param> 513 </param>
514 <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" > 514 <param argument="--skip-tags-regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
515 <expand macro="barcode_sanitizer" /> 515 <expand macro="barcode_sanitizer" />
516 </param> 516 </param>
517 <param argument="--per-contig" type="boolean" truevalue="--per-contig" falsevalue="" label="Deduplicate per contig" help="Field 3 in BAM; RNAME. All reads with the same contig will be considered to have the same alignment position. This is useful if your library prep generates PCR duplicates with non identical alignment positions such as CEL-Seq. In this case, you would align to a reference transcriptome with one transcript per gene" /> 517 <param argument="--per-contig" type="boolean" truevalue="--per-contig" falsevalue="" label="Deduplicate per contig" help="Field 3 in BAM; RNAME. All reads with the same contig will be considered to have the same alignment position. This is useful if your library prep generates PCR duplicates with non identical alignment positions such as CEL-Seq. In this case, you would align to a reference transcriptome with one transcript per gene" />
518 <param argument="--gene-transcript-map" type="data" format="tabular" optional="true" label="Tabular file mapping genes to transripts" /> 518 <param argument="--gene-transcript-map" type="data" format="tabular" optional="true" label="Tabular file mapping genes to transripts" />
519 <param argument="--per-cell" name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" label="Group reads only if they have the same cell barcode" /> 519 <param argument="--per-cell" type="boolean" truevalue="--per-cell" falsevalue="" label="Group reads only if they have the same cell barcode" />
520 </section> 520 </section>
521 </xml> 521 </xml>
522 <token name="@SC_OPTIONS@"><![CDATA[ 522 <token name="@SC_OPTIONS@"><![CDATA[
523 #if str($sc.gene_tag) != "": 523 #if str($sc.gene_tag) != "":
524 --gene-tag '$sc.gene_tag' 524 --gene-tag '$sc.gene_tag'