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comparison metabat2.xml @ 2:708abf08a626 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
author iuc
date Tue, 02 Aug 2022 09:40:59 +0000
parents 76bc4efa1aeb
children eb50e7eca3dc
comparison
equal deleted inserted replaced
1:01f02c5ddff8 2:708abf08a626
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 mkdir bins && 8 mkdir bins &&
9 metabat2 9 metabat2
10 --inFile '$inFile' 10 --inFile '$inFile'
11 --outFile 'bins/bin' 11 --outFile 'bins/bin'
12 #if str($advanced.base_coverage_depth_cond.base_coverage_depth) == 'yes': 12 #if str($advanced.base_coverage_depth_cond.base_coverage_depth) == 'yes'
13 #if $advanced.base_coverage_depth_cond.abdFile: 13 #if $advanced.base_coverage_depth_cond.abdFile
14 --abdFile '$advanced.base_coverage_depth_cond.abdFile' 14 --abdFile '$advanced.base_coverage_depth_cond.abdFile'
15 #else if $advanced.base_coverage_depth_cond.cvExt: 15 #else if $advanced.base_coverage_depth_cond.cvExt
16 --cvExt '$advanced.base_coverage_depth_cond.cvExt' 16 --cvExt '$advanced.base_coverage_depth_cond.cvExt'
17 #end if 17 #end if
18 #end if 18 #end if
19 --minContig $advanced.minContig 19 --minContig $advanced.minContig
20 --maxP $advanced.maxP 20 --maxP $advanced.maxP
21 --minS $advanced.minS 21 --minS $advanced.minS
22 --maxEdges $advanced.maxEdges 22 --maxEdges $advanced.maxEdges
23 --pTNF $advanced.pTNF 23 --pTNF $advanced.pTNF
24 $advanced.noAdd 24 $advanced.noAdd
25 --minCV $advanced.minCV 25 --minCV $advanced.minCV
26 --minCVSum $advanced.minCVSum 26 --minCVSum $advanced.minCVSum
27 --minClsSize $advanced.minClsSize 27 --seed $advanced.seed
28 --numThreads \${GALAXY_SLOTS:-4} 28 --minClsSize $out.minClsSize
29 $advanced.onlyLabel 29 --numThreads \${GALAXY_SLOTS:-4}
30 #if $advanced.saveCls: 30 $out.onlyLabel
31 $advanced.saveCls 31 #if $out.saveCls
32 $out.saveCls
32 --noBinOut 33 --noBinOut
33 #end if 34 #end if
34 $advanced.unbinned 35 #if 'unbinned' in $out.extra_outputs
35 --seed $advanced.seed 36 --unbinned
36 > process_log.txt 37 #end if
37 #if str($advanced.output_process_log) == 'yes': 38 > process_log.txt
39 #if 'log' in $out.extra_outputs
38 && mv process_log.txt '$process_log' 40 && mv process_log.txt '$process_log'
39 #end if 41 #end if
40 ]]></command> 42 ]]></command>
41 <inputs> 43 <inputs>
42 <param argument="--inFile" type="data" format="fasta,fasta.gz" label="Fasta file containing contigs"/> 44 <param argument="--inFile" type="data" format="fasta,fasta.gz" label="Fasta file containing contigs"/>
43 <section name="advanced" title="Advanced options"> 45 <section name="advanced" title="Advanced options">
44 <conditional name="base_coverage_depth_cond"> 46 <conditional name="base_coverage_depth_cond">
45 <param name="base_coverage_depth" type="select" label="Use a base coverage depth file?"> 47 <param name="base_coverage_depth" type="select" label="Use a base coverage depth file?">
48 <option value="yes">Yes</option>
46 <option value="no" selected="true">No</option> 49 <option value="no" selected="true">No</option>
47 <option value="yes">Yes</option>
48 </param> 50 </param>
49 <when value="no"/> 51 <when value="no"/>
50 <when value="yes"> 52 <when value="yes">
51 <param argument="--abdFile" type="data" format="tabular" optional="True" label="Tabular depth matrix file having mean and variance of base coverage depth" help="Generated by the Calculate contig depths for MetaBAT2 tool"/> 53 <param argument="--abdFile" type="data" format="tabular" optional="True" label="Tabular depth matrix file having mean and variance of base coverage depth" help="Generated by the Calculate contig depths for MetaBAT2 tool"/>
52 <param argument="--cvExt" type="data" format="tabular" optional="True" label="Base coverage depth file without variance" help="Generated by a tool - not the Calculate contig depths for MetaBAT2 tool"/> 54 <param argument="--cvExt" type="data" format="tabular" optional="True" label="Base coverage depth file without variance" help="Generated by a tool - not the Calculate contig depths for MetaBAT2 tool"/>
58 <param argument="--maxEdges" type="integer" value="200" label="Maximum number of edges per node" help="The greater, the more sensitive"/> 60 <param argument="--maxEdges" type="integer" value="200" label="Maximum number of edges per node" help="The greater, the more sensitive"/>
59 <param argument="--pTNF" type="integer" value="0" label="TNF probability cutoff for building TNF graph" help="Use it to skip the preparation step (0:auto)"/> 61 <param argument="--pTNF" type="integer" value="0" label="TNF probability cutoff for building TNF graph" help="Use it to skip the preparation step (0:auto)"/>
60 <param argument="--noAdd" type="boolean" truevalue="--noAdd" falsevalue="" checked="false" label="Turn off additional binning for lost or small contigs?"/> 62 <param argument="--noAdd" type="boolean" truevalue="--noAdd" falsevalue="" checked="false" label="Turn off additional binning for lost or small contigs?"/>
61 <param argument="--minCV" type="float" value="1.0" label="Minimum mean coverage of a contig in each library for binning"/> 63 <param argument="--minCV" type="float" value="1.0" label="Minimum mean coverage of a contig in each library for binning"/>
62 <param argument="--minCVSum" type="float" value="1.0" label="Minimum total effective mean coverage of a contig for binning" help="Sum of depth over minCV"/> 64 <param argument="--minCVSum" type="float" value="1.0" label="Minimum total effective mean coverage of a contig for binning" help="Sum of depth over minCV"/>
65 <param argument="--seed" type="integer" value="0" label="For exact reproducibility." help="Zero value will use random seed"/>
66 </section>
67 <section name="out" title="Output options">
63 <param argument="--minClsSize" type="integer" value="200000" label="Minimum size of a bin as the output"/> 68 <param argument="--minClsSize" type="integer" value="200000" label="Minimum size of a bin as the output"/>
64 <param argument="--onlyLabel" type="boolean" truevalue="--onlyLabel" falsevalue="" checked="false" label="Output only sequence labels as a list in a column without sequences?"/> 69 <param argument="--onlyLabel" type="boolean" truevalue="--onlyLabel" falsevalue="" checked="false" label="Output only sequence labels as a list in a column without sequences?"/>
65 <param argument="--saveCls" type="boolean" truevalue="--saveCls" falsevalue="" checked="false" label="Save cluster memberships as a matrix format?"/> 70 <param argument="--saveCls" type="boolean" truevalue="--saveCls" falsevalue="" checked="false" label="Save cluster memberships as a matrix format?"/>
66 <param argument="--unbinned" type="boolean" truevalue="--unbinned" falsevalue="" checked="false" label="Output fasta file containing unbinned contigs?"/> 71 <param name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs">
67 <param argument="--seed" type="integer" value="0" label="For exact reproducibility." help="Zero value will use random seed"/> 72 <option value="lowDepth">Fasta file containing low depth bins (if no matrix format and label selected)</option>
68 <param name="output_process_log" type="select" label="Output process log file?"> 73 <option value="tooShort">Fasta file containing too short bins (if no matrix format and label selected)</option>
69 <option value="no" selected="true">No</option> 74 <option value="unbinned">Fasta file containing unbinned contigs (if no matrix format and label selected)</option>
70 <option value="yes">Yes</option> 75 <option value="log">Process log file</option>
71 </param> 76 </param>
72 </section> 77 </section>
73 </inputs> 78 </inputs>
74 <outputs> 79 <outputs>
75 <collection name="bin_files" type="list" label="${tool.name} on ${on_string}: (bins)"> 80 <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
76 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" format="fasta" directory="bins"/> 81 <filter>not out['saveCls'] and not out['onlyLabel']</filter>
82 <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)\.fa" format="fasta" directory="bins"/>
77 </collection> 83 </collection>
78 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> 84 <data name="bin_saveCls" format="tabular" from_work_dir="bins/bin" label="${tool.name} on ${on_string}: Bins">
79 <filter>advanced['output_process_log'] == 'yes'</filter> 85 <filter>out['saveCls'] and not out['onlyLabel']</filter>
86 </data>
87 <collection name="bin_onlyLabel" type="list" label="${tool.name} on ${on_string}: Bins">
88 <filter>not out['saveCls'] and out['onlyLabel']</filter>
89 <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)" format="tabular" directory="bins"/>
90 </collection>
91 <data name="lowDepth" format="fasta" from_work_dir="bins/bin.lowDepth.fa" label="${tool.name} on ${on_string}: Low depth bins">
92 <filter>not out['saveCls'] and not out['onlyLabel'] and 'lowDepth' in out['extra_outputs']</filter>
93 </data>
94 <data name="tooShort" format="fasta" from_work_dir="bins/bin.tooShort.fa" label="${tool.name} on ${on_string}: Too short bins">
95 <filter>not out['saveCls'] and not out['onlyLabel'] and 'tooShort' in out['extra_outputs']</filter>
96 </data>
97 <data name="unbinned" format="fasta" from_work_dir="bins/bin.unbinned.fa" label="${tool.name} on ${on_string}: Unbinned sequences">
98 <filter>not out['saveCls'] and not out['onlyLabel'] and 'unbinned' in out['extra_outputs']</filter>
99 </data>
100 <data name="process_log" format="txt" label="${tool.name} on ${on_string}: Process log">
101 <filter>'log' in out['extra_outputs']</filter>
80 </data> 102 </data>
81 </outputs> 103 </outputs>
82 <tests> 104 <tests>
105 <test expect_num_outputs="5">
106 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
107 <section name="advanced">
108 <conditional name="base_coverage_depth_cond">
109 <param name="base_coverage_depth" value="no"/>
110 </conditional>
111 <param name="seed" value="345678"/>
112 </section>
113 <section name="out">
114 <param name="extra_outputs" value="lowDepth,tooShort,unbinned,log"/>
115 </section>
116 <output_collection name="bins" type="list" count="2">
117 <element name="1" ftype="fasta">
118 <assert_contents>
119 <has_size value="334554"/>
120 <has_text text=">MW127517.1"/>
121 <has_text text=">MW127521.1"/>
122 </assert_contents>
123 </element>
124 <element name="2" ftype="fasta">
125 <assert_contents>
126 <has_size value="577866"/>
127 <has_text text=">MT810119.1"/>
128 <has_text text=">MW130866.1"/>
129 </assert_contents>
130 </element>
131 </output_collection>
132 <output name="lowDepth" ftype="fasta">
133 <assert_contents>
134 <has_text text=""/>
135 </assert_contents>
136 </output>
137 <output name="tooShort" ftype="fasta">
138 <assert_contents>
139 <has_text text=""/>
140 </assert_contents>
141 </output>
142 <output name="unbinned" ftype="fasta">
143 <assert_contents>
144 <has_text text=">NC_045512.2"/>
145 <has_text text=">MW130872.1"/>
146 </assert_contents>
147 </output>
148 <output name="process_log" ftype="txt">
149 <assert_contents>
150 <has_text text="MetaBAT"/>
151 <has_text text="2 bins (897090 bases in total) formed"/>
152 </assert_contents>
153 </output>
154 </test>
83 <test expect_num_outputs="1"> 155 <test expect_num_outputs="1">
84 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/> 156 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
85 <param name="seed" value="345678"/> 157 <section name="advanced">
86 <output_collection name="bin_files" type="list" count="2"> 158 <conditional name="base_coverage_depth_cond">
87 <element name="bin.1" ftype="fasta"> 159 <param name="base_coverage_depth" value="yes"/>
88 <assert_contents> 160 <param name="abdFile" value="input_depth1.tabular" ftype="tabular"/>
89 <has_size value="334554"/> 161 </conditional>
90 </assert_contents> 162 <param name="seed" value="345678"/>
91 </element> 163 </section>
92 <element name="bin.2" ftype="fasta"> 164 <section name="out">
93 <assert_contents> 165 <param name="onlyLabel" value="false"/>
94 <has_size value="577866"/> 166 <param name="saveCls" value="false"/>
167 <param name="extra_outputs" value=""/>
168 </section>
169 <output_collection name="bins" type="list" count="0"/>
170 </test>
171 <test expect_num_outputs="1">
172 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
173 <section name="advanced">
174 <conditional name="base_coverage_depth_cond">
175 <param name="base_coverage_depth" value="no"/>
176 </conditional>
177 <param name="seed" value="345678"/>
178 </section>
179 <section name="out">
180 <param name="onlyLabel" value="false"/>
181 <param name="saveCls" value="true"/>
182 <param name="extra_outputs" value=""/>
183 </section>
184 <output name="bin_saveCls" ftype="tabular">
185 <assert_contents>
186 <has_text text="NC_045512.2"/>
187 <has_text text="MT810119.1"/>
188 <has_text text="MW130860.1"/>
189 </assert_contents>
190 </output>
191 </test>
192 <test expect_num_outputs="1">
193 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
194 <section name="advanced">
195 <conditional name="base_coverage_depth_cond">
196 <param name="base_coverage_depth" value="no"/>
197 </conditional>
198 <param name="seed" value="345678"/>
199 </section>
200 <section name="out">
201 <param name="onlyLabel" value="true"/>
202 <param name="saveCls" value="false"/>
203 <param name="extra_outputs" value=""/>
204 </section>
205 <output_collection name="bin_onlyLabel" type="list" count="2">
206 <element name="1" ftype="tabular">
207 <assert_contents>
208 <has_text text="MW127518.1"/>
209 <has_text text="MW127521.1"/>
210 </assert_contents>
211 </element>
212 <element name="2" ftype="tabular">
213 <assert_contents>
214 <has_text text="MT810119.1"/>
215 <has_text text="MW130866.1"/>
95 </assert_contents> 216 </assert_contents>
96 </element> 217 </element>
97 </output_collection> 218 </output_collection>
98 </test>
99 <test expect_num_outputs="2">
100 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
101 <param name="base_coverage_depth" value="yes"/>
102 <param name="abdFile" value="input_depth1.tabular" ftype="tabular"/>
103 <param name="seed" value="345678"/>
104 <param name="output_process_log" value="yes"/>
105 <output_collection name="bin_files" type="list" count="0"/>
106 <output name="process_log" file="process_log.txt" ftype="txt"/>
107 </test> 219 </test>
108 </tests> 220 </tests>
109 <help><![CDATA[ 221 <help><![CDATA[
110 **What it does** 222 **What it does**
111 223