Mercurial > repos > iuc > coverm_genome

annotate macros.xml @ 4:c4e3aa19841c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit bc3831e3648809bd3d46611b2a74bd26a17985e5
author iuc
date Fri, 18 Aug 2023 09:22:54 +0000
parents dd96e74908a9
children
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1 <macros>
3
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2 <token name="@TOOL_VERSION@">0.6.1</token>
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3 <token name="@VERSION_SUFFIX@">2</token>
3
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4 <token name="@PROFILE@">22.01</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">coverm</requirement>
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8 </requirements>
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9 </xml>
3
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10 <xml name="bio_tools">
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11 <xrefs>
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12 <xref type="bio.tools">coverm</xref>
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13 </xrefs>
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14 </xml>
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15 <xml name="citation">
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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16 <citations>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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17 <citation type="bibtex">
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18 @misc{githubCoverm,
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19 author = {B J. Woodcroft},
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20 year = {2021},
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21 title = {CoverM},
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22 publisher = {GitHub},
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23 journal = {GitHub repository},
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24 url = {https://github.com/wwood/CoverM}
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25 }
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26 </citation>
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27 </citations>
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28 </xml>
3
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29 <xml name="mapped">
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30 <param name="mapped" type="select" label="Have the reads already been mapped to contigs?">
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31 <option value="mapped">Yes (no read mapping algorithm will be undertaken)</option>
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32 <option value="not-mapped" selected="true">No</option>
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33 </param>
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34 </xml>
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35 <xml name="assembly_mode">
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36 <param name="mode" type="select" label="Assembly mode?" help="Useful to know if contigs have been generated all samples together (co-assembly) or on each sample individually (individual assembly)">
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37 <option value="individual">Individual assembly (1 contig file per sample)</option>
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38 <option value="co" selected="true">Co-assembly (1 contig file for several samples)</option>
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39 </param>
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40 </xml>
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41 <xml name="mapped_params">
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42 <conditional name="mode">
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43 <expand macro="assembly_mode"/>
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44 <when value="individual">
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45 <param argument="--bam-files" type="data" format="bam" label="BAM file(s)" help="These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n)."/>
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46 </when>
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47 <when value="co">
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48 <param argument="--bam-files" type="data" format="bam" multiple="true" label="BAM file(s)" help="These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n)."/>
0
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49 </when>
3
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50 </conditional>
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51 <param argument="--sharded" type="boolean" truevalue="--sharded" falsevalue="" checked="false" label="BAM file(s) read-sorted alignments of a set of reads mapped to multiple reference contig sets?" help="If set, it will choose the best hit for each read pair" />
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52 </xml>
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53 <token name="@BAMS@"><![CDATA[
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54 #if $mapped.mode.mode == 'individual'
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55 #set $fn = 'bam/' + re.sub('[^\s\w\-\\.]', '_', str($mapped.mode.bam_files.element_identifier))
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56 #silent $bam_fp.append( $fn )
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57 ln -s '$mapped.mode.bam_files' '$fn' &&
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58 #else
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59 #for $i, $bam in enumerate($mapped.mode.bam_files)
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60 #set $fn = 'bam/' + re.sub('[^\s\w\-\\.]', '_', str($bam.element_identifier)) + '_' + str($i)
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61 #silent $bam_fp.append( $fn )
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62 ln -s '$bam' '$fn' &&
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63 #end for
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64 #end if
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65 ]]></token>
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66 <xml name="genomic">
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67 <conditional name="genomic">
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68 <param type="select" name="source" label="Source of FASTA files with each genome" >
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69 <option value="history" selected="true">History</option>
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70 <option value="builtin">Built-in</option>
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71 </param>
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72 <when value="history">
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73 <param argument="--genome-fasta-files" type="data" format="fasta" multiple="true" label="FASTA files of each genome"/>
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74 </when>
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75 <when value="builtin">
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76 <param argument="--genome-fasta-files" type="select" multiple="true" label="Reference genome(s)">
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77 <options from_data_table="all_fasta" />
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78 </param>
0
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79 </when>
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80 </conditional>
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81 </xml>
3
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82 <xml name="cond_single_genome">
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83 <conditional name="cond_single_genome">
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84 <param argument="--single-genome" type="select" label="Are all contigs from the same genome?">
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85 <option value="--single-genome">True</option>
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86 <option value="">False</option>
0
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87 </param>
3
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88 <when value="--single-genome"/>
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89 <when value="">
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90 <conditional name="genome_contig_definition">
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91 <param argument="choice" type="select" label="How to get genome names and contig names?">
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92 <option value="default" selected="true">Using default behavior</option>
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93 <option value="genome-definition">Providing a file containing newline-separated list of genome name and contig</option>
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94 <option value="separator">Providing character that separates genome names from contig names in the reference file</option>
0
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95 </param>
3
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96 <when value="default"/>
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97 <when value="genome-definition">
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98 <param argument="--genome-definition" type="data" format="tabular" label="File containing newline-separated list of genome_name and contig, separated by tab, to define the genome of each contig." />
0
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99 </when>
3
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100 <when value="separator">
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101 <param argument="--separator" type="text" label="Character that separates genome names from contig names in the reference file." >
0
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102 <sanitizer>
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103 <valid initial="string.punctuation">
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104 </valid>
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105 </sanitizer>
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106 </param>
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107 </when>
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108 </conditional>
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109 </when>
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110 </conditional>
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111 </xml>
3
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112 <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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113 <xml name="read_type">
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114 <param name="type" type="select" label="Read type" >
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115 <option value="single">Single end</option>
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116 <option value="paired">Paired end</option>
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117 <option value="paired_collection" selected="true">Paired collection</option>
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118 <option value="interleaved">Interleaved</option>
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119 </param>
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120 </xml>
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121 <xml name="individual_assembly_reads">
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122 <conditional name="read_type">
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123 <expand macro="read_type"/>
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124 <when value="single">
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125 <param argument="--single" type="data" format="@INPUT_FORMATS@" label="Single Read" />
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126 </when>
0
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127 <when value="paired">
3
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128 <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" label="Forward FASTA/Q file for mapping" />
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129 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" label="Reverse FASTA/Q file for mapping" />
0
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130 </when>
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131 <when value="paired_collection">
4
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132 <param name="paired_reads" type="data_collection" collection_type="paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
0
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133 </when>
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134 <when value="interleaved">
3
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135 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" label="Interleaved FASTA/Q files for mapping" />
0
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136 </when>
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137 </conditional>
3
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138 </xml>
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139 <xml name="ref_or_genome">
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140 <param name="ref_or_genome" type="select" label="Genome definition">
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141 <option value="contigs" selected="true">From contigs (e.g. concatenated genomes or metagenome assembly)</option>
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142 <option value="genomic">From FASTA files with each genome</option>
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143 </param>
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144 </xml>
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145 <xml name="individual_assembly_reference">
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146 <param argument="--reference" type="data" format="fasta" label="Contigs"/>
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147 </xml>
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148 <token name="@INDIVIDUAL_ASSEMBLY_READS@"><![CDATA[
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149 #set $reads = $mapped.mode.read_type
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150 #if $reads.type == 'single'
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151 #set $fn = "single/" + re.sub('[^\s\w\-\\.]', '_', str($reads.single.element_identifier))
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152 #silent $single_fp.append( $fn )
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153 ln -s '$reads.single' '$single_fp' &&
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154 #else if $reads.type == 'paired'
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155 #set $fn = "fw/" + re.sub('[^\s\w\-\\.]', '_', str($reads.read1.element_identifier))
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156 #silent $fw_fp.append( $fn )
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157 ln -s '$reads.read1' '$fn' &&
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158 #set $fn = "rv/" + re.sub('[^\s\w\-\\.]', '_', str($reads.read2.element_identifier))
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159 ln -s '$reads.read2' '$fn' &&
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160 #silent $rv_fp.append( $fn )
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161 #else if $reads.type == 'paired_collection'
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162 #set $id = re.sub('[^\s\w\-\\.]', '_', str($reads.paired_reads.element_identifier))
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163 #set $fn = "fw/" + $id
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164 #silent $fw_fp.append( $fn )
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165 ln -s '$reads.paired_reads.forward' '$fn' &&
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166 #set $fn = "rv/" + $id
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167 #silent $rv_fp.append( $fn )
4
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168 ln -s '$reads.paired_reads.reverse' '$fn' &&
3
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169 #else if $reads.type == 'interleaved'
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170 #set $fn = "interl/" + re.sub('[^\s\w\-\\.]', '_', str($reads.interleaved.element_identifier))
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171 #silent $interl_fp.append( $fn )
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172 ln -s '$reads.interleaved' '$fn' &&
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173 #end if
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174 ]]></token>
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175 <token name="@INDIVIDUAL_ASSEMBLY_REF@"><![CDATA[
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176 #set $fn = "ref/" + re.sub('[^\s\w\-\\.]', '_', str($ref.element_identifier))
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177 #silent $ref_fp.append( $fn )
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178 ln -s '$ref' '${fn}' &&
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179 ]]></token>
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180 <token name="@GENOME_FOR_READS@"><![CDATA[
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181 #if $mapped.mode.genome.genomic.source == 'history'
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182 #for $i, $genome in enumerate($mapped.mode.genome.genomic.genome_fasta_files)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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183 #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.element_identifier))
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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184 #silent $genome_fp.append( $fn )
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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185 ln -s '$genome' '$fn' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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186 #end for
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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187 #else
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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188 #for $i, $genome in enumerate($mapped.mode.genome.genomic.genome_fasta_files)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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189 #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.fields.path.element_identifier))
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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190 #silent $genome_fp.append( $fn )
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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191 ln -s '$genome' '$fn' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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192 #end for
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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193 #end if
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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194 ]]></token>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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195 <xml name="co_assembly_reads">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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196 <conditional name="read_type">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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197 <expand macro="read_type"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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198 <when value="single">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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199 <param argument="--single" type="data" format="@INPUT_FORMATS@" multiple="true" label="Single Read" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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200 </when>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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201 <when value="paired">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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202 <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" multiple="true" label="Forward FASTA/Q file(s) for mapping" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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203 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" multiple="true" label="Reverse FASTA/Q file(s) for mapping" />
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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204 </when>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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205 <when value="paired_collection">
4
c4e3aa19841c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit bc3831e3648809bd3d46611b2a74bd26a17985e5
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206 <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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207 </when>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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208 <when value="interleaved">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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209 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" multiple="true" label="Interleaved FASTA/Q files(s) for mapping" />
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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210 </when>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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211 </conditional>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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212 </xml>
3
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213 <xml name="co_assembly_reference">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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214 <param argument="--reference" type="data" format="fasta" multiple="true" label="Contigs" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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215 <param argument="--sharded" type="boolean" truevalue="--sharded" falsevalue="" checked="false" label="Mapping reads to references separately as sharded BAMs?" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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216 </xml>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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217 <token name="@CO_ASSEMBLY_READS@"><![CDATA[
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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218 #if $reads.type == 'single'
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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219 #for $i, $read in enumerate($reads.single)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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220 #set $fn = "single/" + re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier)) + "_single_" + str($i) + $extra
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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221 #silent $single_fp.append( $fn )
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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222 ln -s '$read' '$fn' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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223 #end for
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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224 #else if $reads.type == 'paired'
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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225 #for $i, $read in enumerate($reads.read1)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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226 #set $id = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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227 #set $fn = "fw/" + $id + "_paired_" + str($i) + $extra
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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228 #silent $fw_fp.append( $fn )
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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229 ln -s '$read' '$fn' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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230 #end for
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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231 #for $i, $read in enumerate($reads.read2)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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232 #set $id = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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233 #set $fn = "rv/" + $id + "_paired_" + str($i) + $extra
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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234 #silent $rv_fp.append( $fn )
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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235 ln -s '$read' '$fn' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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236 #end for
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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237 #else if $reads.type == 'paired_collection'
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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238 #for $i, $read in enumerate($reads.paired_reads)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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239 #set $id = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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240 #set $fn = "fw/" + $id + "_paired_collection_" + str($i) + $extra
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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241 #silent $fw_fp.append( $fn )
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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242 ln -s '$read.forward' '$fn' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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243 #set $fn = "rv/" + $id + "_paired_collection_" + str($i) + $extra
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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244 #silent $rv_fp.append( $fn )
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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245 ln -s '$read.reverse' '$fn' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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246 #end for
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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247 #else if $reads.type == 'interleaved'
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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248 #for $i, $read in enumerate($reads.interleaved)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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249 #set $id = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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250 #set $fn = "interl/" + $id + "_interleaved_" + str($i) + $extra
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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251 #silent $interl_fp.append( $fn )
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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252 ln -s '$read' '$fn' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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253 #end for
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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254 #end if
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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255 ]]></token>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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256 <token name="@CO_ASSEMBLY_ALL_READS@"><![CDATA[
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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257 #set $reads = $mapped.mode.read_type
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258 #set $extra = ''
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259 @CO_ASSEMBLY_READS@
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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260 #for $j, $s in enumerate($mapped.mode.extra_reads)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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diff changeset
261 #set $reads = $s.read_type
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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262 #set $extra = str($j)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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263 @CO_ASSEMBLY_READS@
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264 #end for
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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diff changeset
265 ]]></token>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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266 <token name="@CO_ASSEMBLY_REF@"><![CDATA[
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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267 #for $i, $ref in enumerate($refs)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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268 #set $fn = "ref/" + re.sub('[^\s\w\-\\.]', '_', str($ref.element_identifier)) + "_" + str($i)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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269 #silent $ref_fp.append( $fn )
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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270 ln -s '$ref' '${fn}' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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271 #end for
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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diff changeset
272 ]]></token>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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273 <xml name="sharded">
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274 <param name="sharded" type="boolean" truevalue="--sharded" falsevalue="" checked="false" label="Input BAM files are read-sorted alignments of a set of reads mapped to multiple reference contig sets. Choose the best hit for each read pair. Otherwise if mapping was carried out: Map reads to each reference, choosing the best hit for each pair." />
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275 </xml>
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276 <xml name="mapping">
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277 <param argument="--mapper" type="select" label="Underlying mapping software used">
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278 <option value="minimap2-sr" selected="true">minimap2 with '-x sr' option</option>
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279 <option value="minimap2-ont">minimap2 with '-x map-ont' option</option>
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280 <option value="minimap2-pb">minimap2 with '-x map-pb' option</option>
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281 <option value="minimap2-no-preset">minimap2 with no '-x' option</option>
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282 <option value="bwa-mem">BWA-MEM using default parameters</option>
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283 </param>
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284 </xml>
3
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285 <xml name="alignment">
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286 <section name="alignment" title="Alignment thresholding" expanded="false">
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287 <param argument="--min-read-aligned-length" type="integer" min="0" value="0"
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288 label="Minimum number of aligned bases" help="Reads with smaller numbers of aligned bases will be excluded" />
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289 <param argument="--min-read-percent-identity" type="float" min="0" max="100" value="0"
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290 label="Minimum overall percent identity" help="Reads with lower overall percent identity will be excluded." />
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291 <param argument="--min-read-aligned-percent" type="float" min="0" max="100" value="0"
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292 label="Minimum aligned base percent" help="Reads with lower percent aligned bases will be excluded" />
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293 <conditional name="proper_pairs_only">
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294 <param argument="--proper-pairs-only" type="select" label="Require reads to be mapped as proper pairs?">
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295 <option value="--proper-pairs-only">Yes</option>
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296 <option value="" selected="true">No</option>
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297 </param>
3
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298 <when value="--proper-pairs-only">
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299 <param argument="--min_read-aligned-length-pair" type="integer" min="0" value="0"
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300 label="Minimum number of aligned bases for pairs" help="Pairs with smaller numbers of aligned bases will be excluded." />
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301 <param argument="--min-read-percent-identity-pair" type="float" min="0" max="100" value="0"
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302 label="Minimum overall percent identity pair for pairs" help="Pairs by lower overall percent identity will be excluded" />
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303 <param argument="--min-read-aligned-percent-pair" type="float" min="0" max="100" value="0"
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304 label="Minimum percent of read aligned bases for pair" help="Pairs with lower reads percent aligned bases will be excluded" />
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305 </when>
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306 <when value=""/>
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307 </conditional>
3
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308 <param argument="--exclude-supplementary" type="boolean" truevalue="--exclude-supplementary" falsevalue="" checked="false"
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309 label="Exclude supplementary alignments"/>
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310 </section>
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311 </xml>
3
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312 <xml name="cov_method_options">
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313 <option value="trimmed_mean">trimmed_mean: Average number of aligned reads overlapping each position after removing the most deeply and shallow-ly covered positions. </option>
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314 <option value="coverage_histogram">coverage_histogram: Histogram of coverage depths</option>
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315 <option value="covered_bases">covered_bases: Number of bases covered by 1 or more reads</option>
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316 <option value="variance">variance: Variance of coverage depths</option>
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317 <option value="length">length: Length of each contig in base pairs</option>
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318 <option value="count">count: Number of reads aligned toq each contig. Note that a single read may be aligned to multiple contigs with supplementary alignments</option>
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319 <option value="metabat">metabat: ("MetaBAT adjusted coverage") Coverage as defined in Kang et al 2015</option>
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320 <option value="reads_per_base">reads_per_base: Number of reads aligned divided by the length of the contig</option>
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321 <option value="rpkm">rpkm: Reads mapped per kilobase of contig, per million mapped reads</option>
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322 <option value="tpm">tpm: Transcripts Per Million as described in Li et al 2010</option>
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323 </xml>
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324 <xml name="coverage_params">
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325 <param argument="--trim-min" type="integer" min="0" value="5" label="Smallest fraction of positions to remove when calculating" help="Only used with trimmed_mean method"/>
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326 <param argument="--trim-max" type="integer" min="0" value="95" label="Maximum fraction of positions to remove when calculating" help="Only used with trimmed_mean method"/>
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327 <param argument="--min-covered-fraction" type="integer" min="0" value="10" label="Minimum covered fraction" help="Genomes with less coverage than this reported as having zero coverage"/>
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328 <param argument="--contig-end-exclusion" type="integer" min="0" value="75" label="Base to exclude at contig ends" help="Bases at the ends of reference sequences will be excluded from calculation"/>
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329 </xml>
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330 <xml name="output_format">
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331 <param argument="--output-format" type="select" label="Shape of output">
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332 <option value="dense" selected="true">Dense for species-by-site</option>
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333 <option value="sparse">Sparse for long format</option>
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334 </param>
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335 </xml>
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336 <xml name="citations">
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337 <citations>
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338 <yield />
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339 </citations>
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340 </xml>
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341 </macros>