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comparison metaspades.xml @ 6:a9b8c9e204ee 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 21:33:56 +0000
parents 3ca2d2a9068c
children f338e9942b27
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5:3ca2d2a9068c 6:a9b8c9e204ee
1 <tool id="metaspades" name="metaSPAdes" version="3.9.0.1"> 1 <tool id="metaspades" name="metaSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>assembler for metagenomics datasets</description> 2 <description>metagenome assembler</description>
3 <xrefs> 3 <macros>
4 <xref type="bio.tools">metaspades</xref> 4 <import>macros.xml</import>
5 </xrefs> 5 </macros>
6 <requirements> 6 <expand macro="requirements"/>
7 <requirement type="package" version="3.9.0">spades</requirement> 7 <expand macro="stdio"/>
8 </requirements> 8 <expand macro="version_command"/>
9 <stdio> 9 <command detect_errors="exit_code"><![CDATA[
10 <exit_code range="1:" />
11 </stdio>
12 <command>
13 <![CDATA[
14 10
15 if [ -n "\$GALAXY_MEMORY_MB" ]; then 11 #set $library = 1
16 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
17 fi &&
18 12
19 ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output 13 @PREPROCESS_INPUT_FILES_MAIN@
20 spades.py -o . --disable-gzip-output --meta $onlyassembler -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250} 14 #if $additional_reads.selector == 'true'
21 #if not $kmer_choice.auto_kmer_choice: 15 @PREPROCESS_INPUT_FILES_ADDITIONAL@
22 -k "$kmer_choice.kmers" 16 #end if
17 @PREPROCESS_NANOPORE_PACBIO_FILES@
18
19 ## run
20 metaspades.py
21 -o 'output'
22 @RESOURCES@
23 @INPUT_READS_MAIN@
24 #if $additional_reads.selector == 'true'
25 @INPUT_READS_ADDITIONAL@
23 #end if 26 #end if
24 ## Sequence files 27 ## reads
25 #set num=1 28 @NANOPORE_PACBIO@
26 #if str( $lib_type ) == "paired_end": 29 ## parameter
27 #set prefix = 'pe' 30 @KMER@
28 #end if 31 @PHREDOFFSET@
29 --$prefix$num-$orientation 32 @PIPELINE_OPTIONS@
30 #for $file in $files 33 ## postprocessing
31 #if $file.file_type.type == "separate" 34 @STATS@
32 --$prefix$num-1 fastq:$file.file_type.fwd_reads 35 @CORRECTED@
33 --$prefix$num-2 fastq:$file.file_type.rev_reads 36 ]]></command>
34 #elif $file.file_type.type == "interleaved"
35 --$prefix$num-12 fastq:$file.file_type.interleaved_reads
36 #elif $file.file_type.type == "paired-collection"
37 --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward
38 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse
39 #end if
40 #end for
41 ]]>
42 </command>
43 <inputs> 37 <inputs>
44 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" /> 38 <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
45 <conditional name="kmer_choice"> 39 <expand macro="input_additional_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
46 <param name="auto_kmer_choice" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Automatically choose k-mer values" help="k-mer choices can be chosen by SPAdes instead of being entered manually" /> 40 <section name="arf" title="Additional read files">
47 <when value="false"> 41 <expand macro="nanopore_pacbio"/>
48 <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." /> 42 </section>
49 </when> 43 <section name="arf" title="Additional read files">
50 <when value="true" /> 44 <expand macro="nanopore_pacbio"/>
51 </conditional> 45 </section>
52 <param name="lib_type" type="select" label="Library type"> 46 <expand macro="kmer"/>
53 <option value="paired_end">Paired-end</option> 47 <expand macro="phred"/>
54 </param> 48 <expand macro="pipeline_options">
55 <param label="Orientation" name="orientation" type="select"> 49 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
56 <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option> 50 </expand>
57 <option value="rf"><![CDATA[<- -> (rf)]]></option> 51 <expand macro="optional_output"/>
58 <option value="ff"><![CDATA[-> -> (ff)]]></option>
59 </param>
60 <repeat name="files" title="Files" min="1">
61 <conditional name="file_type">
62 <param name="type" type="select" label="Select file format">
63 <option value="separate">Separate input files</option>
64 <option value="interleaved">Interleaved files</option>
65 <option value="paired-collection">Paired List Collection</option>
66 </param>
67 <when value="separate">
68 <param name="fwd_reads" type="data" format="fastq,fastq.gz" label="Forward reads" help="FASTQ format" />
69 <param name="rev_reads" type="data" format="fastq,fastq.gz" label="Reverse reads" help="FASTQ format" />
70 </when>
71 <when value="interleaved">
72 <param name="interleaved_reads" type="data" format="fastq,fastq.gz" label="Interleaved paired reads" help="FASTQ format" />
73 </when>
74 <when value="paired-collection">
75 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" format="fastq,fastq.gz" collection_type="paired" help="FASTQ format" />
76 </when>
77 </conditional>
78 </repeat>
79 </inputs> 52 </inputs>
80 <outputs> 53 <outputs>
81 <data name="out_contigs" format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" /> 54 <expand macro="out_ag"/>
82 <data name="out_scaffolds" format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" /> 55 <expand macro="out_ags"/>
83 <data name="out_fastg" format="txt" from_work_dir="assembly_graph.fastg" label="SPAdes assembly graph (fastg)" /> 56 <expand macro="out_cn"/>
84 <data name="out_log" format="txt" from_work_dir="spades.log" label="SPAdes log" /> 57 <expand macro="out_cp"/>
58 <expand macro="out_cr"/>
59 <expand macro="out_cs"/>
60 <expand macro="out_l"/>
61 <expand macro="out_sc"/>
62 <expand macro="out_sp"/>
63 <expand macro="out_ss"/>
85 </outputs> 64 </outputs>
86 <tests> 65 <tests>
87 <test> 66 <!-- #1 single, interlaced, fastq.gz, default parameters -->
88 <param name="sc" value="false" /> 67 <test expect_num_outputs="4">
89 <param name="careful" value="false" /> 68 <conditional name="singlePaired">
90 <param name="kmers" value="33,55" /> 69 <param name="sPaired" value="paired_interlaced"/>
91 <param name="lib_type" value="paired_end" /> 70 <param name="input1" value="ecoli_1K.fastq.gz"/>
92 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" /> 71 </conditional>
93 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" /> 72 <output name="out_ag">
94 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> 73 <assert_contents>
74 <has_n_lines n="36"/>
75 <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106'"/>
76 </assert_contents>
77 </output>
78 <output name="out_ags">
79 <assert_contents>
80 <has_n_lines n="2"/>
81 <has_text_matching expression="S.+"/>
82 </assert_contents>
83 </output>
84 <output name="out_cn">
85 <assert_contents>
86 <has_n_lines n="18"/>
87 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
88 </assert_contents>
89 </output>
90 <output name="out_sc">
91 <assert_contents>
92 <has_n_lines n="18"/>
93 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
94 </assert_contents>
95 </output>
95 </test> 96 </test>
96 <test> 97 <!-- #2 single, separate, fastq, default parameters -->
97 <param name="sc" value="false" /> 98 <test expect_num_outputs="4">
98 <param name="careful" value="false" /> 99 <conditional name="singlePaired">
99 <param name="kmers" value="33,55" /> 100 <param name="sPaired" value="paired"/>
100 <param name="lib_type" value="paired_end" /> 101 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
101 <param name="fwd_reads" value="ecoli_1K_1.fq.gz" ftype="fastq.gz" /> 102 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
102 <param name="rev_reads" value="ecoli_1K_2.fq.gz" ftype="fastq.gz" /> 103 </conditional>
103 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> 104 <output name="out_ag">
105 <assert_contents>
106 <has_n_lines n="36"/>
107 <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106'"/>
108 </assert_contents>
109 </output>
110 <output name="out_ags">
111 <assert_contents>
112 <has_n_lines n="2"/>
113 <has_text_matching expression="S.+"/>
114 </assert_contents>
115 </output>
116 <output name="out_cn">
117 <assert_contents>
118 <has_n_lines n="18"/>
119 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
120 </assert_contents>
121 </output>
122 <output name="out_sc">
123 <assert_contents>
124 <has_n_lines n="18"/>
125 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
126 </assert_contents>
127 </output>
104 </test> 128 </test>
129 <!-- #3 only corrected reads are created as an output -->
130 <test expect_num_outputs="2">
131 <conditional name="singlePaired">
132 <param name="sPaired" value="paired_interlaced"/>
133 <param name="input1" value="ecoli_1K.fastq.gz"/>
134 </conditional>
135 <param name="optional_output" value="cr,l"/>
136 <output_collection name="out_cr" type="list" count="3">
137 <element name="ecoli_1K.fastq.gz_1.00.0_0.cor">
138 <assert_contents>
139 <has_size value="130317" delta="1000"/>
140 </assert_contents>
141 </element>
142 <element name="ecoli_1K.fastq.gz_2.00.0_0.cor">
143 <assert_contents>
144 <has_size value="130317" delta="1000"/>
145 </assert_contents>
146 </element>
147 <element name="ecoli_1K.fastq.gz__unpaired.00.0_0.cor">
148 <assert_contents>
149 <has_size value="20" delta="5"/>
150 </assert_contents>
151 </element>
152 </output_collection>
153 <output name="out_l">
154 <assert_contents>
155 <has_text_matching expression="Thank you for using SPAdes!"/>
156 </assert_contents>
157 </output>
158 </test>
105 </tests> 159 </tests>
106 <help> 160 <help><![CDATA[
107 <![CDATA[ 161 .. class:: infomark
162
108 **What it does** 163 **What it does**
109 164
110 SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes. 165 @HELP_WID@
111 ]]> 166
112 </help> 167 metaSPAdes is a subtool for assembling metagenomic data sets.
113 <citations> 168
114 <citation type="doi">10.1089/cmb.2012.0021</citation> 169 **Input**
115 </citations> 170
171 @HELP_IN@
172
173 **Output**
174
175 @HELP_OUT_AG@
176 @HELP_OUT_AGS@
177 @HELP_OUT_C@
178 @HELP_OUT_CP@
179 @HELP_OUT_CR@
180 @HELP_OUT_CS@
181 @HELP_OUT_L@
182 @HELP_OUT_S@
183 @HELP_OUT_SP@
184 @HELP_OUT_SS@
185
186 **References**
187
188 More information can be found on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/meta-spades>`_.
189 ]]></help>
190 <expand macro="citations">
191 <citation type="doi">10.1101/gr.213959.116</citation>
192 </expand>
116 </tool> 193 </tool>