Mercurial > repos > jjohnson > mixcr
comparison mixcr_analyze.xml @ 0:445a02a846f3 draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mixcr commit cbcfbd75369000bdcf4bf0dc23852dea30672329-dirty
author | jjohnson |
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date | Sat, 23 Mar 2019 20:56:38 -0400 |
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children | b112efe1994a |
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1 <tool id="mixcr_analyze" name="MiXCR Analyze" version="@VERSION@.0"> | |
2 <description>immuno clonotyes from sequence data</description> | |
3 <macros> | |
4 <import>mixcr_macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 #if $imgt.library_selector == 'history': | |
9 #set $libname = $imgt.library.name | |
10 ln -s -f $imgt.library $libname && | |
11 #end if | |
12 #if str( $fastq_input.fastq_input_selector ) == "paired": | |
13 #set $fq1 = $fastq_input.fastq_input1.name | |
14 ln -s -f $fastq_input.fastq_input1 $fq1 && | |
15 #set $fq2 = $fastq_input.fastq_input2.name | |
16 ln -s -f $fastq_input.fastq_input2 $fq2 && | |
17 #else: | |
18 #set $fq1 = $fastq_input.fastq_input1.name | |
19 ln -s -f $fastq_input.fastq_input1 $fq1 && | |
20 #end if | |
21 mixcr analyze $analyze.pipeline --starting-material $starting_material | |
22 #if $analyze.pipeline == 'amplicon': | |
23 --5-end $analyze.primers5end | |
24 --3-end $analyze.primers3end | |
25 --adapters $analyze.adapters | |
26 #end if | |
27 #if $imgt.library_selector == 'history': | |
28 --align "--library $libname" | |
29 #set $taxonId = str($imgt.species).split(':')[0] | |
30 --species $taxonId | |
31 ## #elif $imgt.library_selector == 'cached': | |
32 #else | |
33 --species $imgt.species | |
34 #end if | |
35 $contig_assembly $impute_germline_on_export $only_productive | |
36 --receptor-type $receptor_type | |
37 #if str( $fastq_input.fastq_input_selector ) == "paired": | |
38 $fq1 $fq2 | |
39 #else: | |
40 $fq1 | |
41 #end if | |
42 mixcr_analysis | |
43 ]]></command> | |
44 <inputs> | |
45 <conditional name="analyze"> | |
46 <param name="pipeline" type="select" label="amplicon or shotgun data" help=""> | |
47 <option value="amplicon">amplicon: enriched targeted TCR/IG libraries (5’RACE, Amplicon, Multiplex, etc)</option> | |
48 <option value="shotgun">shotgun: non-enriched RNA-seq or non-targeted genomic data</option> | |
49 </param> | |
50 <when value="amplicon"> | |
51 <param name="primers5end" type="select" label="5’-end of the library."> | |
52 <help> | |
53 There are two possible values: | |
54 no-v-primers — no V gene primers (e.g. 5’RACE with template switch oligo or a like), | |
55 v-primers — V gene single primer / multiple. | |
56 </help> | |
57 <option value="no-v-primers">no-v-primers</option> | |
58 <option value="v-primers">v-primers</option> | |
59 </param> | |
60 <param name="primers3end" type="select" label="3’-end of the library."> | |
61 <help> | |
62 There are three possible values: | |
63 j-primers — J gene single primer / multiplex, | |
64 j-c-intron-primers — J-C intron single primer / multiplex, | |
65 c-primers — C gene single primer / multiplex (e.g. IGHC primers specific to different immunoglobulin isotypes). | |
66 </help> | |
67 <option value="j-primers">j-primers</option> | |
68 <option value="j-c-intron-primers">j-c-intron-primers</option> | |
69 <option value="c-primers">c-primers</option> | |
70 </param> | |
71 <param name="adapters" type="select" label="Presence of PCR primers and/or adapter sequences"> | |
72 <help> | |
73 If sequences of primers used for PCR or adapters are present in sequencing data, | |
74 it may influence the accuracy of V, J and C gene segments identification and CDR3 mapping. | |
75 </help> | |
76 <option value="adapters-present">adapters-present</option> | |
77 <option value="no-adapters">no-adapters</option> | |
78 </param> | |
79 </when> | |
80 <when value="shotgun"/> | |
81 </conditional> | |
82 <param name="starting_material" type="select" label="Type of starting material: RNA or DNA" help=""> | |
83 <option value="rna">RNA</option> | |
84 <option value="dna">DNA</option> | |
85 </param> | |
86 <conditional name="fastq_input"> | |
87 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> | |
88 <option value="single">single-end fastq</option> | |
89 <option value="paired">paired-end fastq</option> | |
90 </param> | |
91 <when value="paired"> | |
92 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Select first set of reads" help="Specify dataset with forward reads"/> | |
93 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Select second set of reads" help="Specify dataset with reverse reads"/> | |
94 </when> | |
95 <when value="single"> | |
96 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" label="Select sequence dataset" help="Specify dataset with single reads"/> | |
97 </when> | |
98 </conditional> | |
99 <conditional name="imgt"> | |
100 <param name="library_selector" type="select" label="Library selector" help="Select between paired and single end data"> | |
101 <option value="builtin">MiXCR builtin library</option> | |
102 <!-- <option value="cached">repseqio IMGT library</option> --> | |
103 <option value="history">history repseqio IMGT library</option> | |
104 </param> | |
105 <when value="builtin"> | |
106 <param name="species" type="text" label="Species"> | |
107 <option value="9606">HomoSapiens</option> | |
108 <option value="MusMusculus">MusMusculus</option> | |
109 <option value="rat">rat</option> | |
110 </param> | |
111 </when> | |
112 <!-- | |
113 <when value="cached"> | |
114 <param name="library" type="select" label="repseqio IMGT library"> | |
115 <options from_data_table="imgt_library"> | |
116 <column name="name" index="1"/> | |
117 <column name="value" index="2"/> | |
118 </options> | |
119 </param> | |
120 <param name="species" type="select" label="Species"> | |
121 <options from_data_table="imgt_library"> | |
122 <column name="name" index="3"/> | |
123 <column name="value" index="3"/> | |
124 <filter type="param_value" ref="library" column="2" /> | |
125 <filter type="multiple_splitter" column="3" separator=","/> | |
126 </options> | |
127 </param> | |
128 </when> | |
129 --> | |
130 <when value="history"> | |
131 <param name="library" type="data" format="imgt.json" label="repseqio IMGT library"> | |
132 <help><![CDATA[ | |
133 Data coming from IMGT server may be used for academic research only, | |
134 provided that it is referred to IMGT®, and cited as:MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments. | |
135 | |
136 MiXCR is free for academic and non-profit use (see License). | |
137 "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)." | |
138 ]]></help> | |
139 </param> | |
140 <param name="species" type="select" label="Species"> | |
141 <options> | |
142 <filter type="data_meta" ref="library" key="taxon_names" /> | |
143 </options> | |
144 </param> | |
145 </when> | |
146 </conditional> | |
147 <param name="contig_assembly" type="boolean" truevalue="--contig-assembly" falsevalue="" checked="false" label="Assemble full receptor sequences." help="This option may slow down the computation."/> | |
148 <param name="impute_germline_on_export" type="boolean" truevalue="--impute-germline-on-export" falsevalue="" checked="false" label="Use germline segments (printed with lowercase letters) for uncovered gene features"/> | |
149 <param name="only_productive" type="boolean" truevalue="--only-productive" falsevalue="" checked="false" label="Filter out-of-frame and stop-codons in export"/> | |
150 <param name="receptor_type" type="select" label="Dedicated receptor type for analysis"> | |
151 <option value="xcr" selected="true">xcr (all T- and B-cell receptor chains are analyzed)</option> | |
152 <option value="tcr">tcr</option> | |
153 <option value="bcr">bcr</option> | |
154 <option value="tra">tra</option> | |
155 <option value="trb">trb</option> | |
156 <option value="trg">trg</option> | |
157 <option value="trd">trd</option> | |
158 <option value="igh">igh</option> | |
159 <option value="igk">igk</option> | |
160 <option value="igl">igl</option> | |
161 </param> | |
162 </inputs> | |
163 <outputs> | |
164 <data name="report" format="txt" label="${tool.name} on ${on_string}: report" from_work_dir="mixcr_analysis.report"/> | |
165 <data name="clonotypes" format="tabular" label="${tool.name} on ${on_string}: clonotypes.ALL" from_work_dir="mixcr_analysis.clonotypes.ALL.txt"> | |
166 <actions> | |
167 <action name="comment_lines" type="metadata" default="1" /> | |
168 <action name="column_names" type="metadata" default="cloneId,cloneCount,cloneFraction,targetSequences,targetQualities,allVHitsWithScore,allDHitsWithScore,allJHitsWithScore,allCHitsWithScore,allVAlignments,allDAlignments,allJAlignments,allCAlignments,nSeqFR1,minQualFR1,nSeqCDR1,minQualCDR1,nSeqFR2,minQualFR2,nSeqCDR2,minQualCDR2,nSeqFR3,minQualFR3,nSeqCDR3,minQualCDR3,nSeqFR4,minQualFR4,aaSeqFR1,aaSeqCDR1,aaSeqFR2,aaSeqCDR2,aaSeqFR3,aaSeqCDR3,aaSeqFR4,refPoints" /> | |
169 </actions> | |
170 </data> | |
171 </outputs> | |
172 <tests> | |
173 <test> | |
174 <conditional name="analyze"> | |
175 <param name="pipeline" value="shotgun"/> | |
176 </conditional> | |
177 <param name="starting_material" value="rna"/> | |
178 <conditional name="fastq_input"> | |
179 <param name="fastq_input_selector" value="paired"/> | |
180 <param name="fastq_input1" value="sample_IGH_R1.fastq" ftype="fastqsanger"/> | |
181 <param name="fastq_input2" value="sample_IGH_R2.fastq" ftype="fastqsanger"/> | |
182 </conditional> | |
183 <conditional name="imgt"> | |
184 <param name="library_selector" value="builtin"/> | |
185 <param name="species" value="9606"/> | |
186 </conditional> | |
187 <param name="contig_assembly" value="True"/> | |
188 <param name="impute_germline_on_export" value="True"/> | |
189 <param name="only_productive" value="False"/> | |
190 <param name="receptor_type" value="xcr"/> | |
191 <output name="report"> | |
192 <assert_contents> | |
193 <has_text text="Final clonotype count" /> | |
194 </assert_contents> | |
195 </output> | |
196 <output name="clonotypes"> | |
197 <assert_contents> | |
198 <has_text text="CARDDGGGKGDYGRLW" /> | |
199 </assert_contents> | |
200 </output> | |
201 </test> | |
202 <test> | |
203 <conditional name="analyze"> | |
204 <param name="pipeline" value="amplicon"/> | |
205 <param name="primers5end" value="v-primers"/> | |
206 <param name="primers3end" value="j-primers"/> | |
207 <param name="adapters" value="no-adapters"/> | |
208 </conditional> | |
209 <param name="starting_material" value="rna"/> | |
210 <conditional name="fastq_input"> | |
211 <param name="fastq_input_selector" value="paired"/> | |
212 <param name="fastq_input1" value="sample_IGH_R1.fastq" ftype="fastqsanger"/> | |
213 <param name="fastq_input2" value="sample_IGH_R2.fastq" ftype="fastqsanger"/> | |
214 </conditional> | |
215 <conditional name="imgt"> | |
216 <param name="library_selector" value="builtin"/> | |
217 <param name="species" value="9606"/> | |
218 </conditional> | |
219 <param name="contig_assembly" value="True"/> | |
220 <param name="impute_germline_on_export" value="True"/> | |
221 <param name="only_productive" value="False"/> | |
222 <param name="receptor_type" value="xcr"/> | |
223 <output name="report"> | |
224 <assert_contents> | |
225 <has_text text="Final clonotype count" /> | |
226 </assert_contents> | |
227 </output> | |
228 <output name="clonotypes"> | |
229 <assert_contents> | |
230 <has_text text="CARDDGGGKGDYGRLW" /> | |
231 </assert_contents> | |
232 </output> | |
233 </test> | |
234 | |
235 </tests> | |
236 <help><![CDATA[ | |
237 **MiXCR** **a universal tool for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data** | |
238 | |
239 MiXCR_ is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR_ efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments. | |
240 | |
241 **MiXCR is free for academic and non-profit use** (see License_). | |
242 | |
243 This tool runs the MiXCR_ analyze_ pipeline. | |
244 Generally, there two distinct types of library preparation which correspond to the two analyze pipelines: | |
245 | |
246 - analyze_ amplicon_ for analysis of targeted TCR/IG library amplification (5’RACE, Amplicon, Multiplex, etc). | |
247 - analyze_ shotgun_ for analysis of random fragments (RNA-Seq, Exome-Seq, etc). | |
248 | |
249 | |
250 MiXCR_ has builtin libraries for human, mouse and rat. Additional compiled IMGT_ libraries can be imported into your Galaxy history as datatype: *imgt.json* from: https://github.com/repseqio/library-imgt/releases | |
251 | |
252 NOTE: The imgt.201822-5.sv4.json.gz release has the rattus genus taxonId:10114 for rat, whereas the mixcr builtin library has the rattus norvegicus species taxId:10116 for rat. If you encounter imgt library loading errors from mixcr, you may have to substitute 10116 for 10114 in the imgt.201822-5.sv4.json.gz file. | |
253 | |
254 **Data coming from IMGT server may be used for academic research only**, provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)." | |
255 | |
256 .. _MiXCR: https://mixcr.readthedocs.io/en/latest/index.html | |
257 .. _analyze: https://mixcr.readthedocs.io/en/latest/analyze.html | |
258 .. _amplicon: https://mixcr.readthedocs.io/en/latest/analyze.html#analysis-of-targeted-tcr-ig-libraries | |
259 .. _shotgun: https://mixcr.readthedocs.io/en/latest/analyze.html#analysis-of-non-enriched-or-random-fragments | |
260 .. _License: https://mixcr.readthedocs.io/en/latest/license.html#license | |
261 .. _IMGT: https://github.com/repseqio/library-imgt/releases | |
262 ]]></help> | |
263 <expand macro="citations" /> | |
264 </tool> |