Mercurial > repos > iuc > spades_metaplasmidspades

comparison metaplasmidspades.xml @ 0:32ab23671cc1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
author iuc
date Sun, 23 Jan 2022 21:34:23 +0000
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children 21da31ed41a1
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-1:000000000000 0:32ab23671cc1
1 <tool id="spades_metaplasmidspades" name="metaplasmidSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>extract and assembly plasmids from metagenomic data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command detect_errors="exit_code"><![CDATA[
10
11 #set $library = 1
12
13 @PREPROCESS_INPUT_FILES_MAIN@
14 #if $additional_reads.selector == 'true'
15 @PREPROCESS_INPUT_FILES_ADDITIONAL@
16 #end if
17 @PREPROCESS_NANOPORE_PACBIO_FILES@
18 @PREPROCESS_SANGER_FILES@
19 @PREPROCESS_CONTIGS_FILES@
20 @PREPROCESS_ASSEMBLY_GRAPH_FILES@
21
22 ## run
23 spades.py --meta --plasmid
24 -o 'output'
25 @RESOURCES@
26 @INPUT_READS_MAIN@
27 #if $additional_reads.selector == 'true'
28 @INPUT_READS_ADDITIONAL@
29 #end if
30 ## reads
31 @NANOPORE_PACBIO@
32 @SANGER@
33 @CONTIGS@
34 @ASSEMBLY_GRAPH@
35 ## parameter
36 @KMER@
37 @PHREDOFFSET@
38 @PIPELINE_OPTIONS@
39 ## postprocessing
40 @STATS@
41 @CORRECTED@
42 ]]></command>
43 <inputs>
44 <expand macro="input_files_paired" format="fastq, fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
45 <expand macro="input_additional_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
46 <section name="arf" title="Additional read files">
47 <expand macro="nanopore_pacbio"/>
48 <expand macro="sanger"/>
49 <expand macro="contigs"/>
50 <expand macro="assembly_graph"/>
51 </section>
52 <expand macro="kmer"/>
53 <expand macro="phred"/>
54 <expand macro="pipeline_options">
55 <option value="--careful">Careful: ties to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option>
56 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
57 </expand>
58 <param name="optional_output" type="select" multiple="true" optional="false" label="Select optional output file(s)" help="Only shown in history if selected here and generated by the specific run.">
59 <option value="cn" selected="true">Contigs</option>
60 <option value="cs">Contigs stats</option>
61 <option value="cr">Corrected reads</option>
62 <option value="sc" selected="true">Scaffolds</option>
63 <option value="ss">Scaffolds stats</option>
64 <option value="l">Log</option>
65 </param>
66 </inputs>
67 <outputs>
68 <expand macro="out_cn"/>
69 <expand macro="out_cr"/>
70 <expand macro="out_cs"/>
71 <expand macro="out_l"/>
72 <expand macro="out_sc"/>
73 <expand macro="out_ss"/>
74 </outputs>
75 <tests>
76 <!--
77 used in a test:
78 multiple libraries: s, pe#-12, pe#-1, pe#-2, pe#-<or>
79 k, phred-offset, disablerr, iontorrent, only-assembler, only-error-correction
80 -->
81
82 <!-- #1 single, separate, fastq.gz, default parameters -->
83 <test expect_num_outputs="2">
84 <conditional name="singlePaired">
85 <param name="sPaired" value="paired"/>
86 <param name="input1" value="pl1.fq.gz"/>
87 <param name="input2" value="pl2.fq.gz"/>
88 </conditional>
89 <output name="out_cn">
90 <assert_contents>
91 <has_n_lines n="163"/>
92 <has_text_matching expression=">NODE\_1\_length\_9689\_cov\_.+"/>
93 </assert_contents>
94 </output>
95 <output name="out_sc">
96 <assert_contents>
97 <has_n_lines n="163"/>
98 <has_text_matching expression=">NODE\_1\_length\_9689.+"/>
99 </assert_contents>
100 </output>
101 </test>
102 <!-- #2 single, separate, fastq, custom parameters -->
103 <test expect_num_outputs="6">
104 <conditional name="singlePaired">
105 <param name="sPaired" value="paired"/>
106 <param name="input1" value="pl1.fq.gz"/>
107 <param name="input2" value="pl2.fq.gz"/>
108 </conditional>
109 <conditional name="kmer_cond">
110 <param name="kmer_sel" value="manual"/>
111 <param name="manual" value="33"/>
112 </conditional>
113 <param name="phred_offset" value="33"/>
114 <param name="optional_output" value="cn,cs,cr,sc,ss,l"/>
115 <output name="out_cn">
116 <assert_contents>
117 <has_n_lines n="162"/>
118 <has_text_matching expression=">NODE\_1\_length\_9645\_cov\_.+"/>
119 </assert_contents>
120 </output>
121 <output name="out_cs">
122 <assert_contents>
123 <has_n_lines n="1"/>
124 <has_text_matching expression="#name&#009;length&#009;coverage"/>
125 </assert_contents>
126 </output>
127 <output_collection name="out_cr" type="list" count="3">
128 <element name="pl1.fq.gz.fastq.00.0_0.cor">
129 <assert_contents>
130 <has_size value="71752" delta="1000"/>
131 </assert_contents>
132 </element>
133 <element name="pl2.fq.gz.fastq.00.0_0.cor">
134 <assert_contents>
135 <has_size value="71752" delta="1000"/>
136 </assert_contents>
137 </element>
138 <element name="pl_unpaired.00.0_0.cor">
139 <assert_contents>
140 <has_size value="423" delta="100"/>
141 </assert_contents>
142 </element>
143 </output_collection>
144 <output name="out_sc">
145 <assert_contents>
146 <has_n_lines n="162"/>
147 <has_text_matching expression=">NODE\_1\_length\_9645\_cov\_.+"/>
148 </assert_contents>
149 </output>
150 <output name="out_ss">
151 <assert_contents>
152 <has_n_lines n="1"/>
153 <has_text_matching expression="#name&#009;length&#009;coverage"/>
154 </assert_contents>
155 </output>
156 <output name="out_l">
157 <assert_contents>
158 <has_text_matching expression="Thank you for using SPAdes!"/>
159 </assert_contents>
160 </output>
161 </test>
162 <!-- #3 -->
163 <test expect_num_outputs="1">
164 <conditional name="singlePaired">
165 <param name="sPaired" value="paired"/>
166 <param name="input1" value="pl1.fq.gz"/>
167 <param name="input2" value="pl2.fq.gz"/>
168 </conditional>
169 <param name="operation_mode" value="--only-assembler"/>
170 <param name="optional_output" value="l"/>
171 <output name="out_l">
172 <assert_contents>
173 <has_text_matching expression="Thank you for using SPAdes!"/>
174 </assert_contents>
175 </output>
176 </test>
177 <!-- #4, only corrected reads are created as an output -->
178 <test expect_num_outputs="2">
179 <conditional name="singlePaired">
180 <param name="sPaired" value="paired"/>
181 <param name="input1" value="pl1.fq.gz"/>
182 <param name="input2" value="pl2.fq.gz"/>
183 </conditional>
184 <param name="operation_mode" value="--only-error-correction"/>
185 <param name="optional_output" value="cr,l"/>
186 <output_collection name="out_cr" type="list" count="3">
187 <element name="pl1.fq.gz.fastq.00.0_0.cor">
188 <assert_contents>
189 <has_size value="71752" delta="1000"/>
190 </assert_contents>
191 </element>
192 <element name="pl2.fq.gz.fastq.00.0_0.cor">
193 <assert_contents>
194 <has_size value="71752" delta="1000"/>
195 </assert_contents>
196 </element>
197 <element name="pl_unpaired.00.0_0.cor">
198 <assert_contents>
199 <has_size value="423" delta="100"/>
200 </assert_contents>
201 </element>
202 </output_collection>
203 <output name="out_l">
204 <assert_contents>
205 <has_text_matching expression="Thank you for using SPAdes!"/>
206 </assert_contents>
207 </output>
208 </test>
209 </tests>
210 <help><![CDATA[
211 .. class:: infomark
212
213 **What it does**
214
215 @HELP_WID@
216
217 metaplasmidSPAdes is a subtool for assembling plasmids from metagenomic data sets.
218
219 **Input**
220
221 @HELP_IN@
222
223 **Output**
224
225 @HELP_OUT_C@
226 @HELP_OUT_CS@
227 @HELP_OUT_CR@
228 @HELP_OUT_L@
229 @HELP_OUT_S@
230 @HELP_OUT_SS@
231
232 **References**
233
234 More information can be found on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/spades>`_.
235 ]]></help>
236 <expand macro="citations">
237 <citation type="doi">10.1101/gr.241299.118</citation>
238 </expand>
239 </tool>