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annotate bwameth.xml @ 7:6da3972210ee draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 8d6c5d539aa6689006776c1f6b2be9067bcf9d23"
author iuc
date Sat, 27 Nov 2021 10:04:48 +0000
parents b4e6819b25ef
children 62f5fab76dfb
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b4e6819b25ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 6d44811a45b4f6fded1ec72450ed300318095ce4"
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1 <tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy1" profile="20.05">
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2 <description>Fast and accurate aligner of BS-Seq reads.</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.2.2</token>
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5 </macros>
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f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement>
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f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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8 </requirements>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
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9 <version_command>bwameth.py --version</version_command>
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10 <command detect_errors="aggressive"><![CDATA[
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11 #if $referenceSource.source != "indexed":
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12 mkdir index_dir &&
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13 ln -s '$referenceSource.reference' index_dir/genome.fa &&
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14 bwameth.py index index_dir/genome.fa &&
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15 #set index="index_dir/genome.fa"
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16 #else
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17 #set index=$referenceSource.index.fields.path
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18 #end if
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19
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20 ## Link in the files with a name that's appropriate
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21 #if str($single_or_paired.single_or_paired_opts) == 'paired':
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22 #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):
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23 #set read1 = "input_f.fastq.gz"
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24 #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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25 #set read1 = "input_f.fastq.bz2"
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26 #else:
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27 #set read1 = "input_f.fastq"
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28 #end if
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29 ln -f -s '${single_or_paired.input_mate1}' ${read1} &&
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30
5
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31 #if $single_or_paired.input_mate2.is_of_type("fastq.gz", "fastqsanger.gz"):
29bdbc353f20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
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32 #set read2 = "input_r.fastq.gz"
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33 #else if $single_or_paired.input_mate2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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34 #set read2 = "input_r.fastq.bz2"
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35 #else:
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36 #set read2 = "input_r.fastq"
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37 #end if
29bdbc353f20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
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38 ln -f -s '${single_or_paired.input_mate2}' ${read2} &&
29bdbc353f20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
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39 #else if str($single_or_paired.single_or_paired_opts) == 'paired_collection':
29bdbc353f20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
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40 #if $single_or_paired.input_mate1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
29bdbc353f20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
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41 #set read1 = "input_f.fastq.gz"
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42 #else if $single_or_paired.input_mate1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
29bdbc353f20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
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43 #set read1 = "input_f.fastq.bz2"
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44 #else:
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45 #set read1 = "input_f.fastq"
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46 #end if
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47 ln -s '${single_or_paired.input_mate1.forward}' ${read1} &&
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48
5
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49 #if $single_or_paired.input_mate1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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50 #set read2 = "input_r.fastq.gz"
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51 #else if $single_or_paired.input_mate1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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52 #set read2 = "input_r.fastq.bz2"
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53 #else:
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54 #set read2 = "input_r.fastq"
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55 #end if
5
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56 ln -s '${single_or_paired.input_mate1.reverse}' ${read2} &&
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57 #else:
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58 #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):
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59 #set read1 = "input_f.fastq.gz"
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60 #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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61 #set read1 = "input_f.fastq.bz2"
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62 #else:
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63 #set read1 = "input_f.fastq"
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64 #end if
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65 ln -f -s '${single_or_paired.input_singles}' ${read1} &&
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66 #end if
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67
5
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68 bwameth.py
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69 -t "\${GALAXY_SLOTS:-4}"
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70 --reference '${index}'
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71
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72 #if str($readGroup).strip():
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73 --read-group '${readGroup}'
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74 #end if
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75
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76 #if $single_or_paired.single_or_paired_opts == 'single':
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77 $read1
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78 #else:
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79 $read1 $read2
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80 #end if
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81 | samtools view --no-PG -u - | samtools sort --no-PG -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam -
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82 ]]></command>
0
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83 <inputs>
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84 <conditional name="referenceSource">
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85 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?">
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86 <option value="history" selected="True">Use one from the history</option>
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87 <option value="indexed">Use a built-in index</option>
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88 </param>
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89 <when value="history">
1
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90 <param name="reference" type="data" format="fasta" label="Select a genome" help="in FASTA format" />
0
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91 </when>
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92 <when value="indexed">
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93 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
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94 <options from_data_table="bwameth_indexes">
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95 <filter type="sort_by" column="2"/>
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96 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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97 </options>
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98 </param>
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99 </when>
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100 </conditional>
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101
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102 <conditional name="single_or_paired">
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103 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
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104 <option value="single">Single-end</option>
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105 <option value="paired">Paired-end</option>
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106 <option value="paired_collection">Paired-end Dataset Collection</option>
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107 </param>
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108 <when value="single">
3
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109 <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ" help="FASTQ file." />
0
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110 </when>
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111 <when value="paired">
3
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112 <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="First read in pair" help="FASTQ file." />
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113 <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Second read in pair" help="FASTQ file." />
0
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114 </when>
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115 <when value="paired_collection">
3
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116 <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." />
0
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117 </when>
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118 </conditional>
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119 <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'">
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120 <sanitizer sanitize="False"/>
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121 </param>
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122 </inputs>
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123 <outputs>
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124 <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" />
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125 </outputs>
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126 <tests>
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127 <test>
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128 <conditional name="referenceSource">
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129 <param name="source" value="history" />
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130 </conditional>
0
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131 <param name="reference" value="ref.fa.gz" />
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132 <param name="single_or_paired_opts" value="paired" />
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133 <param name="input_mate1" value="t_R1.fastq.gz"/>
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134 <param name="input_mate2" value="t_R2.fastq.gz"/>
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135 <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff-->
0
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136 </test>
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137 <test>
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138 <conditional name="referenceSource">
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139 <param name="source" value="history" />
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140 </conditional>
0
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141 <param name="reference" value="ref.fa.gz" />
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142 <param name="single_or_paired_opts" value="paired_collection" />
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143 <param name="input_mate1">
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144 <collection type="paired">
3
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145 <element name="forward" value="t_R1.fastq.gz"/>
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146 <element name="reverse" value="t_R2.fastq.gz"/>
0
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147 </collection>
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148 </param>
6
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149 <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff-->
0
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150 </test>
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151 </tests>
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152 <help><![CDATA[
0
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153
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154 **What it does**
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155
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156 BWA-meth performs alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. The methodology employed for this is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool.
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157 ]]></help>
0
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158 <citations>
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159 <citation type="bibtex">@misc{1401.1129,
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160 Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
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161 Title = {Fast and accurate alignment of long bisulfite-seq reads},
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162 Year = {2014},
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163 Eprint = {arXiv:1401.1129},
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164 }</citation>
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165 </citations>
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166 </tool>