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comparison flair_collapse.xml @ 0:57dc46adf2da draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
author iuc
date Fri, 27 Nov 2020 21:56:08 +0000
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1 <tool id="flair_collapse" name="FLAIR collapse" version="@TOOL_VERSION@" profile="20.01">
2 <description>defines high-confidence isoforms from flair-corrected reads</description>
3
4 <macros>
5 <import>flair_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements" />
9 <expand macro="version_command" />
10
11 <command detect_errors="exit_code"><![CDATA[
12
13 @PREPARE_REF@
14
15 ln -s '$input_query' query.bed &&
16
17 flair.py collapse
18
19 ###########
20 ## Input ##
21 ###########
22
23 -q query.bed
24 -r '$input_reads'
25 -g reference.fa
26 -f '$input_gtf'
27
28 #if $input_promotors:
29 -p '$input_promotors'
30 #end if
31
32 ########################
33 ## Additional Options ##
34 ########################
35
36 -w $additional_options.window
37 -s $additional_options.support
38 $additional_options.stringent
39
40 #if str($additional_options.select_uniqueness):
41 -n str($additional_options.select_uniqueness)
42 #end if
43
44 $additional_options.isoform
45 --max_ends $additional_options.maxends
46 $additional_options.trustends
47
48 #if str($additional_options.select_filter):
49 -e str($additional_options.select_filter)
50 #end if
51
52 #########
53 ## END ##
54 #########
55
56 ]]></command>
57 <inputs>
58 <param name="input_query" argument="-q" type="data" format="bed" label="Corrected Reads as BED file"/>
59 <param name="input_reads" argument="-r" type="data" format="fasta,fastq" label="FASTA/FASTQ file of raw reads"/>
60 <expand macro="reference_interface" />
61 <param name="input_gtf" argument="-f" type="data" format="gtf" label="GTF annotation file"/>
62 <param name="input_promotors" optional="true" argument="-p" type="data" format="bed" label="Promotor BED file to identify full-length reads" />
63
64 <!-- Additional Options -->
65 <section name="additional_options" title="Additional Options">
66 <param name="window" argument="-w" type="integer" min="1" value="100" label="Window Size" help="Window size for comparing TSS/TES (Default=100)" />
67 <param name="support" argument="-s" type="integer" min="1" value="3" label="Supporting Reads" help="Minimum number of supporting reads for an isoform (Default=3)" />
68 <param name="stringent" argument="--stringent" type="boolean" checked="false" truevalue="--stringent" falsevalue="" label="Use Stringent Mode" help="Specify if all supporting reads need to be full-length (80% coverage and spanning 25 bp of the first and last exons) (Default=false)"/>
69 <param name="select_uniqueness" argument="-n" type="select" label="Choose the TSS/TES for each unique set of splice junction." >
70 <option value="" selected="true">No Selection</option>
71 <option value="none">Best TSSs/TESs</option>
72 <option value="longest">Single TSS/TES chosen to maximize length</option>
73 <option value="best_only">Single most supported TSS/TES used in conjunction chosen</option>
74 </param>
75 <param name="isoform" argument="-i" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Use Isoform Mode" help="TSS/TES for each isoform will be determined from supporting reads for individual isoforms (Default=false)"/>
76 <param name="maxends" argument="--max_ends" type="integer" min="0" value="2" label="Maximum Number of TSS/TES picked per isoform" help="(Default=2)" />
77 <param name="trustends" argument="--trust_ends" type="boolean" checked="false" truevalue="--trust_ends" falsevalue="" label="Reads are generated from a long read method with minimal fragmentation?" />
78 <param name="select_filter" argument="-e" type="select" label="Filter for isoforms." >
79 <option value="" selected="true">No Filter</option>
80 <option value="nosubset">Any isoforms that are a proper set of another isoform are removed</option>
81 <option value="default">Subset isoforms are removed based on support</option>
82 <option value="comprehensive">Default set + all subset isoforms</option>
83 <option value="ginormous">Comprehensive set + single exon subset isoforms</option>
84 </param>
85 <param name="mapq" argument="--quality" type="integer" min="0" value="1" label="Minimum MAPQ of read assignment to an isoform" help="(Default=1)" />
86 </section>
87
88 <section name="additional_outputs" title="Output Options">
89 <param name="out_format" type="select" multiple="true" optional="true" display="checkboxes" label="Data types">
90 <option value="bed">BED</option>
91 <option value="fasta">FASTA</option>
92 </param>
93 </section>
94 </inputs>
95
96 <outputs>
97 <data name="outfile_isoforms_gtf" from_work_dir="flair.collapse.isoforms.gtf" format="gtf" label="${tool.name} on ${on_string}: Isoforms GTF" />
98 <data name="outfile_isoforms_bed" from_work_dir="flair.collapse.isoforms.bed" format="bed" label="${tool.name} on ${on_string}: Isoforms BED">
99 <filter>additional_outputs['out_format'] and 'bed' in additional_outputs['out_format']</filter>
100 </data>
101 <data name="outfile_isoforms_fasta" from_work_dir="flair.collapse.isoforms.fa" format="fasta" label="${tool.name} on ${on_string}: Isoforms FASTA">
102 <filter>additional_outputs['out_format'] and 'fasta' in additional_outputs['out_format']</filter>
103 </data>
104 </outputs>
105
106 <tests>
107 <test expect_num_outputs="3">
108 <param name="input_query" ftype="bed" value="flair_all_corrected.bed" />
109 <param name="input_reads" ftype="fastq.gz" value="chrM.fastq.gz" />
110 <param name="ref_selector_genome" value="history" />
111 <param name="reffile" ftype="fasta" value="chrM.fa" />
112 <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" />
113 <param name="out_format" value="bed,fasta" />
114 <output name="outfile_isoforms_gtf" ftype="gtf" file="flair.collapse.isoforms.gtf" />
115 <output name="outfile_isoforms_bed" ftype="bed" file="flair.collapse.isoforms.bed" />
116 <output name="outfile_isoforms_fasta" ftype="fasta" file="flair.collapse.isoforms.fa" />
117 </test>
118 <!-- Test with cached genome -->
119 <test expect_num_outputs="3">
120 <param name="input_query" ftype="bed" value="flair_all_corrected.bed" />
121 <param name="input_reads" ftype="fastq.gz" value="chrM.fastq.gz" />
122 <param name="ref_selector_genome" value="cached" />
123 <param name="reffile" value="chrM" />
124 <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" />
125 <param name="out_format" value="bed,fasta" />
126 <output name="outfile_isoforms_gtf" ftype="gtf" file="flair.collapse.isoforms.gtf" />
127 <output name="outfile_isoforms_bed" ftype="bed" file="flair.collapse.isoforms.bed" />
128 <output name="outfile_isoforms_fasta" ftype="fasta" file="flair.collapse.isoforms.fa" />
129 </test>
130 </tests>
131 <help><![CDATA[
132
133 .. class:: infomark
134
135 **What it does**
136
137 -------------------
138
139 @description@
140
141 **flair collapse**
142 Defines high-confidence isoforms from corrected reads.
143
144 -------------------
145
146 **Inputs**
147
148 -------------------
149
150 (1) Corrected Reads as Bed12 File.
151 (2) FASTA/FASTQ file of raw reads. All raw read fastq/fasta files should be concatenated into a single file.
152 (3) FASTA of Reference Genome.
153 (4) GTF annotation file.
154 (5) Promoter regions bed file to identify full-length reads.
155
156 -----------
157
158 **Outputs**
159
160 -----------
161
162 Outputs the high-confidence isoforms in several formats:
163 (1) bed,
164 (2) gtf,
165 (3) FASTA.
166
167 --------------------
168
169 **More Information**
170
171 --------------------
172
173 See the excellent `FLAIR documentation`_
174
175 .. _`FLAIR documentation`: https://github.com/BrooksLabUCSC/flair
176
177
178 --------------------
179
180 **Galaxy Wrapper Development**
181
182 --------------------
183
184 @citation@
185
186 ]]></help>
187 <expand macro="citations" />
188 </tool>