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comparison jgi_summarize_bam_contig_depths.xml @ 1:1592150e38d2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit f239f2bb562330c955c19c328935793d6f1f2aa7
author iuc
date Fri, 29 Jul 2022 12:37:53 +0000
parents d27a4ed006ee
children a4441f35f17b
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0:d27a4ed006ee 1:1592150e38d2
1 <tool id="metabat2_jgi_summarize_bam_contig_depths" name="Calculate contig depths" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="metabat2_jgi_summarize_bam_contig_depths" name="Calculate contig depths" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>for MetaBAT2</description> 2 <description>for MetaBAT2</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="use_reference">
6 <param name="use_reference" type="select" label="Select a reference genome?">
7 <option value="no" selected="true">No</option>
8 <option value="yes">Yes</option>
9 </param>
10 </xml>
11 <xml name="reference_source">
12 <param name="reference_source" type="select" label="Choose the source for the reference genome">
13 <option value="cached" selected="true">locally cached</option>
14 <option value="history">from history</option>
15 </param>
16 </xml>
17 <xml name="referenceFasta">
18 <param argument="--referenceFasta" type="data" format="fasta,fasta.gz" label="Using reference genome" help="Must be the reference used to map the input bam files"/>
19 </xml>
20 <xml name="gcWindow">
21 <param argument="--gcWindow" type="integer" value ="100" label="Sliding window size for GC calculations"/>
22 </xml>
5 </macros> 23 </macros>
6 <expand macro="requirements"/> 24 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 25 <command detect_errors="exit_code"><![CDATA[
8 jgi_summarize_bam_contig_depths 26 jgi_summarize_bam_contig_depths
9 --outputDepth '$outputDepth' 27 --outputDepth '$outputDepth'
10 --percentIdentity $advanced.percentIdentity 28 --percentIdentity $advanced.percentIdentity
11 #if str($advanced.output_paired_contigs) == 'yes': 29 #if $advanced.output_paired_contigs
12 --pairedContigs '$outputPairedContigs' 30 --pairedContigs '$outputPairedContigs'
13 #end if 31 #end if
14 $advanced.noIntraDepthVariance 32 $advanced.noIntraDepthVariance
15 $advanced.showDepth 33 $advanced.showDepth
16 --minMapQual $advanced.minMapQual 34 --minMapQual $advanced.minMapQual
17 --weightMapQual $advanced.weightMapQual 35 --weightMapQual $advanced.weightMapQual
18 $advanced.includeEdgeBases 36 $advanced.includeEdgeBases
19 --maxEdgeBases $advanced.maxEdgeBases 37 --maxEdgeBases $advanced.maxEdgeBases
20 #if str($advanced.use_reference_cond.use_reference) == 'yes': 38 #if str($mode.use_reference_cond.use_reference) == 'yes'
21 #if str($advanced.use_reference_cond.reference_cond.reference_source) == 'cached' 39 #if str($mode.use_reference_cond.reference_cond.reference_source) == 'cached'
22 --referenceFasta '$advanced.use_reference_cond.reference_cond.referenceFasta.fields.path' 40 --referenceFasta '$mode.use_reference_cond.reference_cond.referenceFasta.fields.path'
23 #else: 41 #else
24 --referenceFasta '$advanced.use_reference_cond.reference_cond.referenceFasta' 42 --referenceFasta '$mode.use_reference_cond.reference_cond.referenceFasta'
25 #end if 43 #end if
26 --outputGC '$outputGC' 44 --outputGC '$outputGC'
27 --gcWindow $advanced.use_reference_cond.gcWindow 45 --gcWindow $mode.use_reference_cond.gcWindow
28 --outputReadStats '$outputReadStats' 46 --outputReadStats '$outputReadStats'
29 --outputKmers '$outputKmers' 47 --outputKmers '$outputKmers'
30 #end if 48 #end if
31 --shredLength $shredding.shredLength 49 --shredLength $shredding.shredLength
32 --shredDepth $shredding.shredDepth 50 --shredDepth $shredding.shredDepth
33 --minContigLength $shredding.minContigLength 51 --minContigLength $shredding.minContigLength
34 --minContigDepth $shredding.minContigDepth 52 --minContigDepth $shredding.minContigDepth
35 #for bam_input in $bam_inputs: 53 #if $mode.type == 'individual'
54 '$mode.bam_indiv_input'
55 #else
56 #for $bam_input in $mode.bam_co_inputs
36 '$bam_input' 57 '$bam_input'
37 #end for 58 #end for
59 #end if
38 ]]></command> 60 ]]></command>
39 <inputs> 61 <inputs>
40 <param name="bam_inputs" type="data" format="bam" multiple="true" label="Sorted bam files"/> 62 <conditional name="mode">
63 <param name="type" type="select" label="Mode to process BAM files">
64 <option value="individual">One by one</option>
65 <option value="co">Together</option>
66 </param>
67 <when value="individual">
68 <param name="bam_indiv_input" type="data" format="bam" label="Sorted bam files"/>
69 <conditional name="use_reference_cond">
70 <expand macro="use_reference"/>
71 <when value="no"/>
72 <when value="yes">
73 <conditional name="reference_cond">
74 <expand macro="reference_source"/>
75 <when value="cached">
76 <param argument="--referenceFasta" type="select" label="Using reference genome">
77 <options from_data_table="fasta_indexes">
78 <filter type="data_meta" column="1" key="dbkey" ref="bam_indiv_input"/>
79 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected BAM file(s)"/>
80 </options>
81 </param>
82 </when>
83 <when value="history">
84 <expand macro="referenceFasta"/>
85 </when>
86 </conditional>
87 <expand macro="gcWindow"/>
88 </when>
89 </conditional>
90 </when>
91 <when value="co">
92 <param name="bam_co_inputs" type="data" format="bam" multiple="true" label="Sorted bam files"/>
93 <conditional name="use_reference_cond">
94 <expand macro="use_reference"/>
95 <when value="no"/>
96 <when value="yes">
97 <conditional name="reference_cond">
98 <expand macro="reference_source"/>
99 <when value="cached">
100 <param argument="--referenceFasta" type="select" label="Using reference genome">
101 <options from_data_table="fasta_indexes">
102 <filter type="data_meta" column="1" key="dbkey" ref="bam_co_inputs"/>
103 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected BAM file(s)"/>
104 </options>
105 </param>
106 </when>
107 <when value="history">
108 <expand macro="referenceFasta"/>
109 </when>
110 </conditional>
111 <expand macro="gcWindow"/>
112 </when>
113 </conditional>
114 </when>
115 </conditional>
41 <section name="advanced" title="Advanced options"> 116 <section name="advanced" title="Advanced options">
42 <param argument="--percentIdentity" type="integer" value="97" label="Minimum end-to-end percent identity of qualifying reads"/> 117 <param argument="--percentIdentity" type="integer" value="97" label="Minimum end-to-end percent identity of qualifying reads"/>
43 <param name="output_paired_contigs" type="select" display="radio" label="Output the sparse matrix of contigs which paired reads span?"> 118 <param name="output_paired_contigs" type="boolean" checked="false" label="Output the sparse matrix of contigs which paired reads span?"/>
44 <option value="no" selected="true">No</option>
45 <option value="yes">Yes</option>
46 </param>
47 <param argument="--noIntraDepthVariance" type="boolean" truevalue="--noIntraDepthVariance" falsevalue="" checked="false" label="Remove variance from mean depth along the contig?"/> 119 <param argument="--noIntraDepthVariance" type="boolean" truevalue="--noIntraDepthVariance" falsevalue="" checked="false" label="Remove variance from mean depth along the contig?"/>
48 <param argument="--showDepth" type="boolean" truevalue="--showDepth" falsevalue="" checked="false" label="Output a depth file per bam for each contig base?"/> 120 <param argument="--showDepth" type="boolean" truevalue="--showDepth" falsevalue="" checked="false" label="Output a depth file per bam for each contig base?"/>
49 <param argument="--minMapQual" type="integer" value="0" label="Minimum mapping quality necessary to count a read as mapped"/> 121 <param argument="--minMapQual" type="integer" value="0" label="Minimum mapping quality necessary to count a read as mapped"/>
50 <param argument="--weightMapQual" type="float" value="0.0" label="Weight per-base depth based on the MQ of the read" help="Zero value disables"/> 122 <param argument="--weightMapQual" type="float" value="0.0" label="Weight per-base depth based on the MQ of the read" help="Zero value disables"/>
51 <param argument="--includeEdgeBases" type="boolean" truevalue="--includeEdgeBases" falsevalue="" checked="false" label="Include 1-readlength edges when calculating depth and variance?"/> 123 <param argument="--includeEdgeBases" type="boolean" truevalue="--includeEdgeBases" falsevalue="" checked="false" label="Include 1-readlength edges when calculating depth and variance?"/>
52 <param argument="--maxEdgeBases" type="integer" value="75" label="Maximum length when calculating depth and variance" help="Ignored when including 1-readlength edges when calculating depth and variance"/> 124 <param argument="--maxEdgeBases" type="integer" value="75" label="Maximum length when calculating depth and variance" help="Ignored when including 1-readlength edges when calculating depth and variance"/>
53 <conditional name="use_reference_cond"> 125
54 <param name="use_reference" type="select" label="Select a reference genome?">
55 <option value="no" selected="true">No</option>
56 <option value="yes">Yes</option>
57 </param>
58 <when value="no"/>
59 <when value="yes">
60 <conditional name="reference_cond">
61 <param name="reference_source" type="select" label="Choose the source for the reference genome">
62 <option value="cached" selected="true">locally cached</option>
63 <option value="history">from history</option>
64 </param>
65 <when value="cached">
66 <param argument="--referenceFasta" type="select" label="Using reference genome">
67 <options from_data_table="fasta_indexes">
68 <filter type="data_meta" column="1" key="dbkey" ref="bam_inputs"/>
69 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected BAM file(s)"/>
70 </options>
71 </param>
72 </when>
73 <when value="history">
74 <param argument="--referenceFasta" type="data" format="fasta,fasta.gz" label="Using reference genome" help="Must be the reference used to map the input bam files"/>
75 </when>
76 </conditional>
77 <param argument="--gcWindow" type="integer" value ="100" label="Sliding window size for GC calculations"/>
78 </when>
79 </conditional>
80 </section> 126 </section>
81 <section name="shredding" title="Options to control shredding contigs that are under-represented by the reads"> 127 <section name="shredding" title="Options to control shredding contigs that are under-represented by the reads">
82 <param argument="--shredLength" type="integer" value="16000" label="Maximum length of the shreds"/> 128 <param argument="--shredLength" type="integer" value="16000" label="Maximum length of the shreds"/>
83 <param argument="--shredDepth" type="integer" value="5" label="Depth to generate overlapping shreds"/> 129 <param argument="--shredDepth" type="integer" value="5" label="Depth to generate overlapping shreds"/>
84 <param argument="--minContigLength" type="integer" value="1" label="Mimimum length of contig to include for mapping and shredding"/> 130 <param argument="--minContigLength" type="integer" value="1" label="Mimimum length of contig to include for mapping and shredding"/>
85 <param argument="--minContigDepth" type="float" value="0.0" label="Minimum depth along the contig at which to break the contig"/> 131 <param argument="--minContigDepth" type="float" value="0.0" label="Minimum depth along the contig at which to break the contig"/>
86 </section> 132 </section>
87 </inputs> 133 </inputs>
88 <outputs> 134 <outputs>
89 <data name="outputDepth" format="tabular" label="${tool.name} on ${on_string} (depth matrix)"/> 135 <data name="outputDepth" format="tabular" label="${tool.name} on ${on_string}: Depth matrix"/>
90 <data name="outputPairedContigs" format="fasta" label="${tool.name} on ${on_string} (paired contigs)"> 136 <data name="outputPairedContigs" format="fasta" label="${tool.name} on ${on_string}: Paired contigs">
91 <filter>advanced["output_paired_contigs"] == "yes"</filter> 137 <filter>advanced["output_paired_contigs"]</filter>
92 </data> 138 </data>
93 <data name="outputGC" format="tabular" label="${tool.name} on ${on_string} (gc coverage histogram)"> 139 <data name="outputGC" format="tabular" label="${tool.name} on ${on_string}: GC coverage histogram">
94 <filter>advanced["use_reference_cond"]["use_reference"] == "yes"</filter> 140 <filter>mode["use_reference_cond"]["use_reference"] == 'yes'</filter>
95 </data> 141 </data>
96 <data name="outputReadStats" format="tabular" label="${tool.name} on ${on_string} (read statistics)"> 142 <data name="outputReadStats" format="tabular" label="${tool.name} on ${on_string}: Read statistics">
97 <filter>advanced["use_reference_cond"]["use_reference"] == "yes"</filter> 143 <filter>mode["use_reference_cond"]["use_reference"] == 'yes'</filter>
98 </data> 144 </data>
99 <data name="outputKmers" format="tabular" label="${tool.name} on ${on_string} (perfect kmer counts)"> 145 <data name="outputKmers" format="tabular" label="${tool.name} on ${on_string}: Perfect kmer counts">
100 <filter>advanced["use_reference_cond"]["use_reference"] == "yes"</filter> 146 <filter>mode["use_reference_cond"]["use_reference"] == 'yes'</filter>
101 </data> 147 </data>
102 </outputs> 148 </outputs>
103 <tests> 149 <tests>
104 <!-- Single input, default settings --> 150 <!-- Single input, default settings -->
105 <test expect_num_outputs="1"> 151 <test expect_num_outputs="1">
106 <param name="bam_inputs" value="input1.bam" ftype="bam"/> 152 <conditional name="mode">
153 <param name="type" value="individual"/>
154 <param name="bam_indiv_input" value="input1.bam" ftype="bam"/>
155 </conditional>
107 <output name="outputDepth" file="jgi_output1.tabular" ftype="tabular" compare="contains"/> 156 <output name="outputDepth" file="jgi_output1.tabular" ftype="tabular" compare="contains"/>
108 </test> 157 </test>
109 <!-- Multiple inputs, default settings --> 158 <!-- Multiple inputs, default settings -->
110 <test expect_num_outputs="1"> 159 <test expect_num_outputs="1">
111 <param name="bam_inputs" value="input1.bam,input1.bam" ftype="bam"/> 160 <conditional name="mode">
161 <param name="type" value="co"/>
162 <param name="bam_co_inputs" value="input1.bam,input1.bam" ftype="bam"/>
163 </conditional>
112 <output name="outputDepth" file="jgi_output2.tabular" ftype="tabular" compare="contains"/> 164 <output name="outputDepth" file="jgi_output2.tabular" ftype="tabular" compare="contains"/>
113 </test> 165 </test>
114 <!-- Single input, output paired contigs, reference from history --> 166 <!-- Single input, output paired contigs, reference from history -->
115 <test expect_num_outputs="5"> 167 <test expect_num_outputs="5">
116 <param name="bam_inputs" value="input2.bam" ftype="bam" dbkey="89"/> 168 <conditional name="mode">
117 <param name="output_paired_contigs" value="yes"/> 169 <param name="type" value="individual"/>
118 <param name="use_reference" value="yes"/> 170 <param name="bam_indiv_input" value="input2.bam" ftype="bam" dbkey="89"/>
119 <param name="reference_source" value="history"/> 171 <conditional name="use_reference_cond">
120 <param name="referenceFasta" value="NC_002945v4.fasta" ftype="fasta"/> 172 <param name="use_reference" value="yes"/>
173 <conditional name="reference_cond">
174 <param name="reference_source" value="history"/>
175 <param name="referenceFasta" value="NC_002945v4.fasta" ftype="fasta"/>
176 </conditional>
177 </conditional>
178 </conditional>
179 <section name="advanced">
180 <param name="output_paired_contigs" value="true"/>
181 </section>
121 <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/> 182 <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/>
122 <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/> 183 <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/>
123 <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/> 184 <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/>
124 <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/> 185 <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/>
125 <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/> 186 <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/>
126 </test> 187 </test>
127 <!-- Single input, output paired contigs, cached reference --> 188 <!-- Single input, output paired contigs, cached reference -->
128 <test expect_num_outputs="5"> 189 <test expect_num_outputs="5">
129 <param name="bam_inputs" value="input2.bam" ftype="bam" dbkey="89"/> 190 <conditional name="mode">
130 <param name="output_paired_contigs" value="yes"/> 191 <param name="type" value="individual"/>
131 <param name="use_reference" value="yes"/> 192 <param name="bam_indiv_input" value="input2.bam" ftype="bam" dbkey="89"/>
132 <param name="reference_source" value="cached"/> 193 <conditional name="use_reference_cond">
194 <param name="use_reference" value="yes"/>
195 <conditional name="reference_cond">
196 <param name="reference_source" value="cached"/>
197 </conditional>
198 </conditional>
199 </conditional>
200 <section name="advanced">
201 <param name="output_paired_contigs" value="true"/>
202 </section>
133 <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/> 203 <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/>
134 <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/> 204 <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/>
135 <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/> 205 <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/>
136 <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/> 206 <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/>
137 <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/> 207 <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/>
138 </test> 208 </test>
139 </tests> 209 </tests>
140 <help> 210 <help><![CDATA[
141 **What it does** 211 **What it does**
142 212
143 Calculates coverage depth for each sequence in one or more selected BAM files, producing a tabular file (for each input) 213 Calculates coverage depth for each sequence in one or more selected BAM files, producing a tabular file (for each input)
144 having mean and variance of base coverage depth that can be used as one of the inputs for the MetaBAT2 metagenome binning 214 having mean and variance of base coverage depth that can be used as one of the inputs for the MetaBAT2 metagenome binning
145 tool. 215 tool.
170 240
171 **Options** 241 **Options**
172 242
173 * **Select a reference genome** - optionally select the reference genome that was used to map the input bam file(s) and 3 additional outputs will be produced; gc coverage histogram, read statistics and perfect kmer counts. 243 * **Select a reference genome** - optionally select the reference genome that was used to map the input bam file(s) and 3 additional outputs will be produced; gc coverage histogram, read statistics and perfect kmer counts.
174 244
175 </help> 245 ]]></help>
176 <expand macro="citations"/> 246 <expand macro="citations"/>
177 </tool> 247 </tool>
178 248