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comparison maxbin2.xml @ 5:8a0473eb465e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
author iuc
date Fri, 17 Jun 2022 17:27:40 +0000
parents 4ef88f9a195d
children 2bc40bfbcfb4
comparison
equal deleted inserted replaced
4:4ef88f9a195d 5:8a0473eb465e
1 <tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy2"> 1 <tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy3">
2 <description>clusters metagenomic contigs into bins</description> 2 <description>clusters metagenomic contigs into bins</description>
3 <xrefs>
4 <xref type="bio.tools">masigpro</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <token name="@MAXBIN_VERSION@">2.2.7</token> 7 <token name="@MAXBIN_VERSION@">2.2.7</token>
8 <xml name="contig">
9 <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>
10 </xml>
11 <xml name="input_type">
12 <param name="type" type="select" label="Input type">
13 <option value="reads" selected="true">Sequencing Reads</option>
14 <option value="abund">Abundances</option>
15 </param>
16 </xml>
17 <xml name="reads_extra_params">
18 <param name="output_abundances" type="boolean" checked="false" label="Output abundances" help="" />
19 <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="Reassembly" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." />
20 </xml>
5 </macros> 21 </macros>
6 <requirements> 22 <requirements>
7 <requirement type="package" version="@MAXBIN_VERSION@">maxbin2</requirement> 23 <requirement type="package" version="@MAXBIN_VERSION@">maxbin2</requirement>
8 </requirements> 24 </requirements>
9 <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command> 25 <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>
10 <command detect_errors="exit_code"><![CDATA[ 26 <command detect_errors="exit_code"><![CDATA[
11 ## generate read or abundance files 27 ## generate read or abundance files
12 #if $intype_cond.intype_select == 'rds': 28 #if $assembly.inputs.type == 'reads'
13 #for $r in $intype_cond.reads 29 #if $assembly.type == 'individual'
30 echo '$assembly.inputs.reads' >> reads_list &&
31 #else
32 #for $r in $assembly.inputs.reads
14 #if $r 33 #if $r
15 echo '$r' >> reads_list && 34 echo '$r' >> reads_list &&
16 #end if
17 #end for
18 #else if $intype_cond.intype_select == 'abdc':
19 #for $a in $intype_cond.abund
20 #if $a
21 echo '$a' >> abund_list &&
22 #end if 35 #end if
23 #end for 36 #end for
24 #end if 37 #end if
25 38 #else if $assembly.inputs.type == 'abund'
26 ## in case of reassembly the IBDA out and err is appended 39 #if $assembly.type == 'individual'
27 ## to differentiate this a header is added also befor the 40 echo '$assembly.inputs.abund' >> abund_list &&
28 ## MaxBin2 outputs 41 #else
29 #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != "" 42 #for $a in $assembly.inputs.abund
30 echo "==== MaxBin2 stdout ====" && 43 #if $a
31 echo "==== MaxBin2 stderr ====" 1>&2 && 44 echo '$a' >> abund_list &&
45 #end if
46 #end for
32 #end if 47 #end if
33 48 #end if
34 run_MaxBin.pl 49
50 ## in case of reassembly the IBDA out and err is appended
51 ## to differentiate this a header is added also befor the
52 ## MaxBin2 outputs
53 #if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
54 echo "==== MaxBin2 stdout ====" &&
55 echo "==== MaxBin2 stderr ====" 1>&2 &&
56 #end if
57
58 run_MaxBin.pl
35 -contig '$contig' 59 -contig '$contig'
36 -out out 60 -out out
37 #if $intype_cond.intype_select == 'rds': 61 #if $assembly.inputs.type == 'reads':
38 -reads_list reads_list 62 -reads_list reads_list
39 $intype_cond.reassembly 63 $assembly.inputs.reassembly
40 #else if $intype_cond.intype_select == 'abdc': 64 #else if $assembly.inputs.type == 'abund':
41 -abund_list abund_list 65 -abund_list abund_list
42 #end if 66 #end if
43 #if $adv_cond.adv_select == 'yes': 67 -min_contig_length $adv.min_contig_length
44 -min_contig_length $adv_cond.min_contig_length 68 -max_iteration $adv.max_iteration
45 -max_iteration $adv_cond.max_iteration 69 -prob_threshold $adv.prob_threshold
46 -prob_threshold $adv_cond.prob_threshold 70 $output.plotmarker
47 $adv_cond.plotmarker 71 -markerset $output.markerset
48 -markerset $adv_cond.markerset
49 #end if
50 -thread \${GALAXY_SLOTS:-1} 72 -thread \${GALAXY_SLOTS:-1}
51 73
52 && gzip -cd out.marker_of_each_bin.tar.gz | tar -xf - 74 && gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -
53 75
54 ## redirect the idba out and err file content to stdout and err 76 ## redirect the idba out and err file content to stdout and err
55 ## since this is also wanted in case the error case ';' is used here to 77 ## since this is also wanted in case the error case ';' is used here to
56 ## separate commands 78 ## separate commands
57 #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != "" 79 #if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
58 ; echo "==== IDBA stdout ====" 80 ; echo "==== IDBA stdout ===="
59 && if [[ -f out.idba.out ]]; then cat out.idba.out; fi 81 && if [[ -f out.idba.out ]]; then cat out.idba.out; fi
60 && echo "==== IDBA stderr ====" 1>&2 82 && echo "==== IDBA stderr ====" 1>&2
61 && if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi 83 && if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi
62 #end if 84 #end if
63 ]]></command> 85 ]]></command>
64 <inputs> 86 <inputs>
65 <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/> 87 <expand macro="contig"/>
66 <conditional name="intype_cond"> 88 <conditional name="assembly">
67 <param name="intype_select" type="select" label="Input type"> 89 <param name="type" type="select" label="Assembly type used to generate contig(s)">
68 <option value="rds" selected="true">Sequencing Reads</option> 90 <option value="individual">Assembly of sample(s) one by one (individual assembly)</option>
69 <option value="abdc">Abundances</option> 91 <option value="coassembly">Assembly of different samples together (co-assembly)</option>
70 </param>
71 <when value="rds">
72 <param name="reads" type="data" format="fasta,fastq" multiple="true" label="Reads file(s)" help="(-read/-read2/...)"/>
73 <param name="output_abundances" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output abundances" help="" />
74 <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="Reassembly" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." />
75 </when>
76 <when value="abdc">
77 <param name="abund" type="data" format="tabular" multiple="true" label="Abundance file(s)" help="(-abund/-abund2/...)" />
78 </when>
79 </conditional>
80 <conditional name="adv_cond">
81 <param name="adv_select" type="select" label="Advanced options">
82 <option value="yes">Yes</option>
83 <option value="no" selected="true">No</option>
84 </param> 92 </param>
85 <when value="no"/> 93 <when value="individual">
86 <when value="yes"> 94 <conditional name="inputs">
87 <param argument="-min_contig_length" type="integer" min="0" value="1000" label="minimum contig length" /> 95 <expand macro="input_type"/>
88 <param argument="-max_iteration" type="integer" min="0" value="50" label="Maximum Expectation-Maximization algorithm iteration number" /> 96 <when value="reads">
89 <param argument="-prob_threshold" type="float" min="0" max="1.0" value="0.5" label="Probability threshold for EM final classification" /> 97 <param argument="-reads" type="data" format="fasta,fastq" label="Reads file"/>
90 <param argument="-plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" /> 98 <expand macro="reads_extra_params"/>
91 <param name="output_marker" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output marker gene presence for bins table" /> 99 </when>
92 <param name="output_markers" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output marker genes for each bin as fasta" /> 100 <when value="abund">
93 <param name="output_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log" /> 101 <param argument="-abund" type="data" format="tabular" label="Abundance file"/>
94 <param argument="-markerset" type="select" label="Marker gene set"> 102 </when>
95 <option value="107" selected="true">107 marker genes present in >95% of bacteria</option> 103 </conditional>
96 <option value="40">40 marker gene sets that are universal among bacteria and archaea</option> 104 </when>
97 </param> 105 <when value="coassembly">
106 <conditional name="inputs">
107 <expand macro="input_type"/>
108 <when value="reads">
109 <param argument="-reads" type="data" multiple="true" format="fasta,fastq" label="Reads file(s)"/>
110 <expand macro="reads_extra_params"/>
111 </when>
112 <when value="abund">
113 <param argument="-abund" type="data" format="tabular" multiple="true" label="Abundance file(s)"/>
114 </when>
115 </conditional>
98 </when> 116 </when>
99 </conditional> 117 </conditional>
118 <section name="adv" title="Advanced options">
119 <param argument="-min_contig_length" type="integer" min="0" value="1000" label="minimum contig length" />
120 <param argument="-max_iteration" type="integer" min="0" value="50" label="Maximum Expectation-Maximization algorithm iteration number" />
121 <param argument="-prob_threshold" type="float" min="0" max="1.0" value="0.5" label="Probability threshold for EM final classification" />
122 </section>
123 <section name="output" title="Outputs">
124 <param argument="-plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" />
125 <param name="marker" type="boolean" checked="false" label="Output marker gene presence for bins table" />
126 <param name="markers" type="boolean" checked="false" label="Output marker genes for each bin as fasta" />
127 <param name="log" type="boolean" checked="false" label="Output log" />
128 <param argument="-markerset" type="select" label="Marker gene set">
129 <option value="107" selected="true">107 marker genes present in >95% of bacteria</option>
130 <option value="40">40 marker gene sets that are universal among bacteria and archaea</option>
131 </param>
132 </section>
100 </inputs> 133 </inputs>
101 <outputs> 134 <outputs>
102 <!-- default outputs --> 135 <!-- default outputs -->
103 <collection name="bins" type="list" label="${tool.name} on ${on_string} (bins)"> 136 <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
104 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" /> 137 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
105 </collection> 138 </collection>
106 <data name="noclass" format="fasta" label="${tool.name} on ${on_string} (unclassified sequences)" from_work_dir="out.noclass"/> 139 <data name="noclass" format="fasta" label="${tool.name} on ${on_string}: Unclassified sequences" from_work_dir="out.noclass"/>
107 <data name="toshort" format="fasta" label="${tool.name} on ${on_string} (to short sequences)" from_work_dir="out.tooshort"/> 140 <data name="toshort" format="fasta" label="${tool.name} on ${on_string}: Too short sequences" from_work_dir="out.tooshort"/>
108 <data name="summary" format="tabular" label="${tool.name} on ${on_string} (summary)" from_work_dir="out.summary"/> 141 <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" from_work_dir="out.summary"/>
109
110 <!-- optional outputs --> 142 <!-- optional outputs -->
111 <data name="log" format="txt" label="${tool.name} on ${on_string} (log)" from_work_dir="out.log"> 143 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="out.log">
112 <filter>adv_cond['adv_select']=='yes' and adv_cond['output_log']</filter> 144 <filter>output['log']</filter>
113 </data> 145 </data>
114 <data name="marker" format="tabular" label="${tool.name} on ${on_string} (marker gene presence)" from_work_dir="out.marker"> 146 <data name="marker" format="tabular" label="${tool.name} on ${on_string}: Marker gene presence" from_work_dir="out.marker">
115 <filter>adv_cond['adv_select']=='yes' and adv_cond['output_marker']</filter> 147 <filter>output['marker']</filter>
116 </data> 148 </data>
117 <data name="abundout" format="tabular" label="${tool.name} on ${on_string} (abundances)" from_work_dir="out.abund1"> 149 <data name="abundout" format="tabular" label="${tool.name} on ${on_string}: Abundances" from_work_dir="out.abund1">
118 <filter>intype_cond['intype_select']=='rds' and intype_cond['output_abundances']</filter> 150 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['output_abundances']</filter>
119 </data> 151 </data>
120 <data name="plot" format="pdf" label="${tool.name} on ${on_string} (marker gene presence plot)" from_work_dir="out.marker.pdf"> 152 <data name="plot" format="pdf" label="${tool.name} on ${on_string}: Marker gene presence plot" from_work_dir="out.marker.pdf">
121 <filter>adv_cond['adv_select']=='yes' and adv_cond['plotmarker']</filter> 153 <filter>output['plotmarker']</filter>
122 </data> 154 </data>
123 <collection name="markers" type="list" label="${tool.name} on ${on_string} (markers prediced for bins)"> 155 <collection name="markers" type="list" label="${tool.name} on ${on_string}: Markers prediced for bins">
124 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).marker.fasta" format="fasta" visible="false" /> 156 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).marker.fasta" format="fasta" visible="false" />
125 <filter>adv_cond['adv_select']=='yes' and adv_cond['output_markers']</filter> 157 <filter>output['markers']</filter>
126 </collection> 158 </collection>
127
128 <!-- additional output in case of reassembly --> 159 <!-- additional output in case of reassembly -->
129 <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string} (reassembly bins)"> 160 <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string}: Reassembly bins">
130 <discover_datasets directory="out.reassem" pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" /> 161 <discover_datasets directory="out.reassem" pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
131 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter> 162 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
132 </collection> 163 </collection>
133 <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string} (reassembly reads)"> 164 <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string}: Reassembly reads">
134 <discover_datasets directory="out.reassem" pattern="out.reads.(?P&lt;designation&gt;[0-9]+)" format="fasta" visible="false" /> 165 <discover_datasets directory="out.reassem" pattern="out.reads.(?P&lt;designation&gt;[0-9]+)" format="fasta" visible="false" />
135 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter> 166 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
136 </collection> 167 </collection>
137 <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string} (reassembly unclassified sequences)" from_work_dir="out.reassem/out.reads.noclass"> 168 <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string}: Reassembly unclassified sequences" from_work_dir="out.reassem/out.reads.noclass">
138 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter> 169 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
139 </data> 170 </data>
140 <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string} (reassembly N50)" from_work_dir="out.reassem/N50.txt"> 171 <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string}: Reassembly N50" from_work_dir="out.reassem/N50.txt">
141 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter> 172 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
142 </data> 173 </data>
143 </outputs> 174 </outputs>
144 <tests> 175 <tests>
145 <!-- test w contigs and reads as input --> 176 <!-- test w contigs and reads as input -->
146 <test expect_num_outputs="4"> 177 <test expect_num_outputs="4">
147 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" /> 178 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
148 <conditional name="intype_cond"> 179 <conditional name="assembly">
149 <param name="intype_select" value="rds"/> 180 <param name="type" value="individual"/>
150 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/> 181 <conditional name="inputs">
182 <param name="type" value="reads"/>
183 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
184 <param name="output_abundances" value="false"/>
185 <param name="reassembly" value=""/>
186 </conditional>
151 </conditional> 187 </conditional>
152 <conditional name="adv_cond"> 188 <section name="adv">
153 <param name="adv_select" value="no"/> 189 <param name="min_contig_length" value="1000"/>
154 </conditional> 190 <param name="max_iteration" value="50"/>
191 <param name="prob_threshold" value="0.5"/>
192 </section>
193 <section name="output">
194 <param name="plotmarker" value=""/>
195 <param name="marker" value="false"/>
196 <param name="markers" value="false" />
197 <param name="log" value="false"/>
198 <param name="markerset" value="107"/>
199 </section>
155 <output_collection name="bins" type="list" count="2"> 200 <output_collection name="bins" type="list" count="2">
156 <element name="001" file="1/out.001.fasta" ftype="fasta"/> 201 <element name="001" file="1/out.001.fasta" ftype="fasta"/>
157 <element name="002" file="1/out.002.fasta" ftype="fasta"/> 202 <element name="002" file="1/out.002.fasta" ftype="fasta"/>
158 </output_collection> 203 </output_collection>
159 <output name="summary" file="1/out.summary" ftype="tabular" /> 204 <output name="summary" file="1/out.summary" ftype="tabular" />
160 <output name="noclass" file="1/out.noclass" ftype="fasta" /> 205 <output name="noclass" file="1/out.noclass" ftype="fasta" />
161 <output name="toshort" file="1/out.tooshort" ftype="fasta" /> 206 <output name="toshort" file="1/out.tooshort" ftype="fasta" />
162 </test> 207 </test>
163 <!-- test w contigs and reads as input test for optional outputs --> 208 <!-- test w co-assembled contigs and multiple reads and optional outputs -->
164 <test expect_num_outputs="9"> 209 <test expect_num_outputs="9">
165 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" /> 210 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
166 <conditional name="intype_cond"> 211 <conditional name="assembly">
167 <param name="intype_select" value="rds"/> 212 <param name="type" value="coassembly"/>
168 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/> 213 <conditional name="inputs">
169 <param name="output_abundances" value="true" /> 214 <param name="type" value="reads"/>
215 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta,interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
216 <param name="output_abundances" value="true"/>
217 <param name="reassembly" value=""/>
218 </conditional>
170 </conditional> 219 </conditional>
171 <conditional name="adv_cond"> 220 <section name="adv">
172 <param name="adv_select" value="yes"/> 221 <param name="min_contig_length" value="1000"/>
173 <param name="plotmarker" value="true" /> 222 <param name="max_iteration" value="50"/>
174 <param name="output_marker" value="true" /> 223 <param name="prob_threshold" value="0.5"/>
175 <param name="output_markers" value="true" /> 224 </section>
176 <param name="output_log" value="true" /> 225 <section name="output">
177 </conditional> 226 <param name="plotmarker" value="true"/>
227 <param name="marker" value="true"/>
228 <param name="markers" value="true" />
229 <param name="log" value="true"/>
230 <param name="markerset" value="107"/>
231 </section>
178 <output_collection name="bins" type="list" count="2"> 232 <output_collection name="bins" type="list" count="2">
179 <element name="001" file="1/out.001.fasta" ftype="fasta"/> 233 <element name="001" file="1/out.001.fasta" ftype="fasta"/>
180 <element name="002" file="1/out.002.fasta" ftype="fasta"/> 234 <element name="002" file="1/out.002.fasta" ftype="fasta"/>
181 </output_collection> 235 </output_collection>
182 <output name="summary" file="1/out.summary" ftype="tabular" /> 236 <output name="summary" ftype="tabular">
237 <assert_contents>
238 <has_text text="Completeness"/>
239 <has_text text="out.001.fasta"/>
240 </assert_contents>
241 </output>
183 <output name="noclass" file="1/out.noclass" ftype="fasta" /> 242 <output name="noclass" file="1/out.noclass" ftype="fasta" />
184 <output name="toshort" file="1/out.tooshort" ftype="fasta" /> 243 <output name="toshort" file="1/out.tooshort" ftype="fasta" />
185 <output name="log" file="1/out.log" ftype="txt" compare="diff" lines_diff="21" /> 244 <output name="log" ftype="txt" >
245 <assert_contents>
246 <has_text text="Input contig"/>
247 <has_text text="Elapsed time"/>
248 <has_text text="Yielded 2 bins for contig (scaffold) file"/>
249 </assert_contents>
250 </output>
186 <output name="abundout" file="1/out.abund1" ftype="tabular" /> 251 <output name="abundout" file="1/out.abund1" ftype="tabular" />
187 <output name="marker" file="1/out.marker" ftype="tabular" /> 252 <output name="marker" file="1/out.marker" ftype="tabular" />
188 <output name="plot" file="1/out.marker.pdf" ftype="pdf" compare="sim_size" /> 253 <output name="plot" file="1/out.marker.pdf" ftype="pdf" compare="sim_size" />
189 <output_collection name="markers" type="list" count="1"> 254 <output_collection name="markers" type="list" count="1">
190 <element name="001" file="1/out.001.marker.fasta" ftype="fasta"/> 255 <element name="001" file="1/out.001.marker.fasta" ftype="fasta"/>
191 </output_collection> 256 </output_collection>
192 </test> 257 </test>
193 <!--test w contigs and abundances as input + advanced options --> 258 <!--test w contigs and abundances as input + advanced options -->
194 <test expect_num_outputs="5"> 259 <test expect_num_outputs="5">
195 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" /> 260 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
196 <conditional name="intype_cond"> 261 <conditional name="assembly">
197 <param name="intype_select" value="abdc"/> 262 <param name="type" value="individual"/>
198 <param name="abund" value="abundances.tsv" ftype="tabular"/> 263 <conditional name="inputs">
264 <param name="type" value="abund"/>
265 <param name="abund" value="abundances.tsv" ftype="tabular"/>
266 </conditional>
199 </conditional> 267 </conditional>
200 <conditional name="adv_cond"> 268 <section name="adv">
201 <param name="adv_select" value="yes"/>
202 <param name="min_contig_length" value="500"/> 269 <param name="min_contig_length" value="500"/>
203 <param name="max_iteration" value="10"/> 270 <param name="max_iteration" value="10"/>
204 <param name="prob_threshold" value="0.95"/> 271 <param name="prob_threshold" value="0.95"/>
272 </section>
273 <section name="output">
205 <param name="plotmarker" value="-plotmarker"/> 274 <param name="plotmarker" value="-plotmarker"/>
275 <param name="marker" value="false"/>
276 <param name="markers" value="false" />
277 <param name="log" value="false"/>
206 <param name="markerset" value="107"/> 278 <param name="markerset" value="107"/>
207 </conditional> 279 </section>
208 <output_collection name="bins" type="list" count="2"> 280 <output_collection name="bins" type="list" count="2">
209 <element name="001" file="2/out.001.fasta" ftype="fasta"/> 281 <element name="001" file="2/out.001.fasta" ftype="fasta"/>
210 <element name="002" file="2/out.002.fasta" ftype="fasta"/> 282 <element name="002" file="2/out.002.fasta" ftype="fasta"/>
211 </output_collection> 283 </output_collection>
212 <output name="summary" file="2/out.summary" ftype="tabular" /> 284 <output name="summary" file="2/out.summary" ftype="tabular" />
215 <output name="plot" file="2/out.marker.pdf" ftype="pdf" compare="sim_size" /> 287 <output name="plot" file="2/out.marker.pdf" ftype="pdf" compare="sim_size" />
216 </test> 288 </test>
217 <!-- test w contigs and reads as input + reassembly--> 289 <!-- test w contigs and reads as input + reassembly-->
218 <test expect_num_outputs="8"> 290 <test expect_num_outputs="8">
219 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" /> 291 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
220 <conditional name="intype_cond"> 292 <conditional name="assembly">
221 <param name="intype_select" value="rds"/> 293 <param name="type" value="individual"/>
222 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/> 294 <conditional name="inputs">
223 <param name="reassembly" value="-reassembly"/> 295 <param name="type" value="reads"/>
296 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
297 <param name="output_abundances" value="false"/>
298 <param name="reassembly" value="-reassembly"/>
299 </conditional>
224 </conditional> 300 </conditional>
225 <conditional name="adv_cond"> 301 <section name="adv">
226 <param name="adv_select" value="no"/> 302 <param name="min_contig_length" value="1000"/>
227 </conditional> 303 <param name="max_iteration" value="50"/>
304 <param name="prob_threshold" value="0.5"/>
305 </section>
306 <section name="output">
307 <param name="plotmarker" value=""/>
308 <param name="marker" value="false"/>
309 <param name="markers" value="false" />
310 <param name="log" value="false"/>
311 <param name="markerset" value="107"/>
312 </section>
228 <output_collection name="bins" type="list" count="2"> 313 <output_collection name="bins" type="list" count="2">
229 <element name="001" file="3/out.001.fasta" ftype="fasta"/> 314 <element name="001" file="3/out.001.fasta" ftype="fasta"/>
230 <element name="002" file="3/out.002.fasta" ftype="fasta"/> 315 <element name="002" file="3/out.002.fasta" ftype="fasta"/>
231 </output_collection> 316 </output_collection>
232 <output name="summary" file="3/out.summary" ftype="tabular" /> 317 <output name="summary" file="3/out.summary" ftype="tabular" />
233 <output name="noclass" file="3/out.noclass" ftype="fasta" /> 318 <output name="noclass" file="3/out.noclass" ftype="fasta" />
234 <output name="toshort" file="3/out.tooshort" ftype="fasta" /> 319 <output name="toshort" file="3/out.tooshort" ftype="fasta" />
235 <output_collection name="reassembly_bins" type="list" count="2"> 320 <output_collection name="reassembly_bins" type="list" count="2">
236 <element name="001" file="3/out.reassem/out.001.fasta" ftype="fasta"/> 321 <element name="001" ftype="fasta">
237 <element name="002" file="3/out.reassem/out.002.fasta" ftype="fasta"/> 322 <assert_contents>
323 <has_text text=">scaffold_0"/>
324 <has_text text=">scaffold_523"/>
325 </assert_contents>
326 </element>
327 <element name="002" ftype="fasta">
328 <assert_contents>
329 <has_text text=">scaffold_0"/>
330 <has_text text=">scaffold_523"/>
331 </assert_contents>
332 </element>
238 </output_collection> 333 </output_collection>
239 <output_collection name="reassembly_reads" type="list" count="2"> 334 <output_collection name="reassembly_reads" type="list" count="2">
240 <element name="001" file="3/out.reassem/out.reads.001" ftype="fasta"/> 335 <element name="001" file="3/out.reassem/out.reads.001" ftype="fasta"/>
241 <element name="002" file="3/out.reassem/out.reads.002" ftype="fasta"/> 336 <element name="002" file="3/out.reassem/out.reads.002" ftype="fasta"/>
242 </output_collection> 337 </output_collection>
243 <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" /> 338 <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" />
244 <output name="reassembly_n50" file="3/out.reassem/N50.txt" ftype="txt" /> 339 <output name="reassembly_n50" ftype="txt">
340 <assert_contents>
341 <has_text text="N50 before reassem"/>
342 <has_text text="out.002.fasta"/>
343 <has_text text="2878"/>
344 </assert_contents>
345 </output>
245 </test> 346 </test>
246 </tests> 347 </tests>
247 <help><![CDATA[ 348 <help><![CDATA[
248 MaxBin is a software that clusters metagenomic contigs into different bins, 349 MaxBin is a software that clusters metagenomic contigs into different bins,
249 each consists (hopefully) of contigs from one species. MaxBin uses the 350 each consists (hopefully) of contigs from one species. MaxBin uses the