annotate alleyoop.xml @ 3:24657d5edede draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 11770937d250d7a332875becf06b9a42b17c46d1
author iuc
date Mon, 21 Jan 2019 16:47:01 -0500
parents 57bf9a0d49a5
children 141f65f7c7c8
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1 <tool id="alleyoop" name="Alleyoop" version="@TOOL_VERSION@">
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2 <description>- post-processing and QC of Slamdunk analyses</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <version_command>alleyoop --version</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
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11 #if $reference_source.reference_source_selector == 'history':
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12 ln -f -s '$reference_source.ref_file' reference.fa &&
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13 #else:
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14 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
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15 #end if
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16
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17 mkdir ./filter &&
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18 #for $bam in $reads:
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19 #set $ext = ""
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20 #set $bam_name = re.sub('[^\w\-\.]', '_', str($bam.element_identifier))
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21 #if not $bam_name.endswith('.bam')
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22 #set $ext = ".bam"
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23 #end if
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24 ln -s '$bam' './filter/${bam_name}${ext}' &&
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25 ln -s '$bam.metadata.bam_index' './filter/${bam_name}${ext}.bai' &&
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26 #end for
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28 mkdir ./count &&
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29 #for $tsv in $count_tsvs:
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30 #set $ext = ""
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31 #set $tsv_name = re.sub('[^\w\-\.]', '_', str($tsv.element_identifier))
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32 #if not $tsv_name.endswith('_tcount.tsv')
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33 #set $ext = "_tcount.tsv"
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34 #end if
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35 ln -s '$tsv' './count/${tsv_name}${ext}' &&
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36 #end for
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37
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38 mkdir ./snp &&
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39 #for $vcf in $variants:
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40 #set $ext = ""
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41 #set $vcf_name = re.sub('[^\w\-\.]', '_', str($vcf.element_identifier))
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42 #if not $vcf_name.endswith('_snp.vcf')
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43 #set $ext = "_snp.vcf"
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44 #end if
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45 ln -s '$vcf' './snp/${vcf_name}${ext}' &&
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46 #end for
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47
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48 alleyoop summary -o ./summary.txt -t ./count ./filter/*bam &&
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49
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50 alleyoop rates -o ./stats -r reference.fa -mq $mq ./filter/*bam &&
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51
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52 alleyoop utrrates -o ./stats -r reference.fa -b $Reference -t \${GALAXY_SLOTS:-1} -l $l -mq $mq ./filter/*bam &&
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53
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54 alleyoop tcperreadpos -o ./stats -r reference.fa -s ./snp -t \${GALAXY_SLOTS:-1} -l $l -mq $mq ./filter/*bam &&
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55
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56 alleyoop tcperutrpos -o ./stats -r reference.fa -s ./snp -t \${GALAXY_SLOTS:-1} -l $l -b $Reference -mq $mq ./filter/*bam
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57
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58 #if $bams:
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59 && alleyoop read-separator -o ./splitbams -s ./snp -r reference.fa ./filter/*bam
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60 #end if
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61
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62 ]]></command>
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63 <inputs>
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64 <expand macro="reference_files" />
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65 <param name="reads" type="data" format="sam,bam" multiple="True" label="Slamdunk BAM files" />
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66 <param name="count_tsvs" type="data" format="tabular" multiple="True" label="Slamdunk Count TSV files" />
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67 <param name="variants" type="data" format="vcf" multiple="True" label="Slamdunk VCF files" />
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68 <param argument="-mq" type="integer" label="Minimum base quality"
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69 value="27" min="0"
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70 help="Minimum base quality for T>C conversions (default: 27)." />
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71 <param argument="-l" type="integer" label="Read length"
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72 value="50" min="50" help="Maximum read length (before trimming)." />
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73 <param name="bams" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output T>C separated BAM files?" help="If this option is set to Yes, the Alleyoop read-separator module will be run to output BAM files of separated T>C reads from non T>C reads. Default: No"/>
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74 </inputs>
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75 <outputs>
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76 <collection name="outputSummary" type="list" label="${tool.name} on ${on_string}: Summary tables">
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77 <discover_datasets pattern="(?P&lt;name&gt;.+)\.txt$" format="tabular" directory="." visible="false" />
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78 </collection>
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79 <collection name="outputStats" type="list" label="${tool.name} on ${on_string}: Stats tables">
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80 <discover_datasets pattern="(?P&lt;name&gt;.+)\.csv$" format="tabular" directory="./stats" visible="false" />
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81 </collection>
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82 <collection name="outputTCReads" type="list" label="${tool.name} on ${on_string}: TC Reads">
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83 <discover_datasets pattern="(?P&lt;name&gt;.+)_TCReads.bam$" format="bam" directory="./splitbams" visible="false" />
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84 <filter>bams</filter>
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85 </collection>
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86 <collection name="outputbkgdReads" type="list" label="${tool.name} on ${on_string}: Background Reads">
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87 <discover_datasets pattern="(?P&lt;name&gt;.+)_backgroundReads.bam$" format="bam" directory="./splitbams" visible="false" />
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88 <filter>bams</filter>
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89 </collection>
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90 </outputs>
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91 <tests>
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92 <!-- Ensure default output works -->
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93 <test expect_num_outputs="2">
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94 <param name="reference_source_selector" value="history" />
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95 <param name="ref_file" ftype="fasta" value="ref.fa" />
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96 <param name="Reference" ftype="bed" value="actb.bed" />
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97 <param name="reads" ftype="bam" value="reads1.bam,reads2.bam" />
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98 <param name="count_tsvs" ftype="tabular" value="reads1_tcount.tsv,reads2_tcount.tsv" />
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99 <param name="variants" ftype="vcf" value="reads1_snp.vcf,reads2_snp.vcf" />
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100 <param name="l" value="100" />
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101 <param name="mq" value="27" />
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102 <output_collection name="outputSummary" count="2">
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103 <element name="summary" ftype="tabular" file="summary.txt" />
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104 </output_collection>
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105 <output_collection name="outputStats" count="8">
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106 <element name="reads1_overallrates" ftype="tabular" file="reads1_overallrates.csv" />
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107 </output_collection>
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108 </test>
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109 <!-- Ensure BAM output works -->
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110 <test expect_num_outputs="4">
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111 <param name="reference_source_selector" value="history" />
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112 <param name="ref_file" ftype="fasta" value="ref.fa" />
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113 <param name="Reference" ftype="bed" value="actb.bed" />
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114 <param name="reads" ftype="bam" value="reads1.bam,reads2.bam" />
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115 <param name="count_tsvs" ftype="tabular" value="reads1_tcount.tsv,reads2_tcount.tsv" />
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116 <param name="variants" ftype="vcf" value="reads1_snp.vcf,reads2_snp.vcf" />
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117 <param name="l" value="100" />
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118 <param name="mq" value="27" />
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119 <param name="bams" value="True" />
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120 <output_collection name="outputTCReads" count="2">
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121 <element name="reads1" ftype="bam" file="reads1_TCReads.bam" />
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122 </output_collection>
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123 <output_collection name="outputbkgdReads" count="2">
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124 <element name="reads1" ftype="bam" file="reads1_backgroundReads.bam" />
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125 </output_collection>
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126 </test>
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127 </tests>
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128 <help><![CDATA[
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129 SLAMseq
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130 =======
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131
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132 SLAMseq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. When combined with metabolic labeling protocols, SLAM-seq allows to study the intracellular RNA dynamics, from transcription, RNA processing to RNA stability.
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133
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134 Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 <https://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4435.html>`_
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135
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136 Alleyoop
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137 ========
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138
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139 Alleyoop (Additional sLamdunk heLpEr tools for anY diagnOstics Or Plots) is a collection of tools for post-processing and running diagnostics on Slamdunk analyses. This tool works on the output of the **Slamdunk** tool and requires all the inputs listed in the table below.
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140
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141 =============== ==========================================================================================================================================================
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142 Parameter Description
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143 =============== ==========================================================================================================================================================
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144 **Genome** The reference fasta file (Genome assembly).
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145 **Reference** BED-file containing coordinates for 3' UTRs.
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146 **Reads** Slamdunk Filtered BAM files.
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147 **Counts** Slamdunk Count TSV files.
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148 **Variants** Slandunk VCF files.
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149 **Read length** Maximum length of reads (usually 50, 100, 150).
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150 =============== ==========================================================================================================================================================
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151
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152 This tool runs the **Alleyoop** *summary*, *rates*, *utrrates*, *tcperreadpos* and *tcperutrpos* modules and outputs:
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153
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154 * Tab-separated *summary* files from the summary module with mapping and PCA statistics
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155 * Tab-separated *stats* files from the rates, utrrates, tcperreadpos and tcperutrpos modules
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156
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157 Optionally, the *read-separator* module can be run to output BAM files of separated T>C and non T>C reads.
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158
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159 The summary and stats files can be summarised and visualised with MultiQC. An example MultiQC report can be seen here_. For information on these modules see the `Alleyoop documentation`_.
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160
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161 .. _`Alleyoop documentation`: http://t-neumann.github.io/slamdunk/docs.html#document-Alleyoop
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162 .. _here: http://t-neumann.github.io/slamdunk/multiqc_example/multiqc_report.html
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163
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164 ]]></help>
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165 <citations>
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166 <expand macro="citations" />
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167 </citations>
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168 </tool>