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annotate psiclass.xml @ 0:1b690aa060f6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass commit 2dc6baaeb2d595cbd8d8ffe3bf22b199a0ba23e4
author iuc
date Tue, 26 Sep 2023 16:51:18 +0000
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1b690aa060f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass commit 2dc6baaeb2d595cbd8d8ffe3bf22b199a0ba23e4
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1 <tool id="psiclass" name="PsiCLASS" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>reference-based transcriptome assembler</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 <xrefs>
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7 <xref type="bio.tools">psiclass</xref>
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8 </xrefs>
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9 <expand macro="requirements" />
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10 <command detect_errors='exit_code'><![CDATA[
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11 mkdir -p "annotation_files" &&
1b690aa060f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass commit 2dc6baaeb2d595cbd8d8ffe3bf22b199a0ba23e4
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12 #set $bam_filenames = []
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13 #for $i,$file in enumerate($bam_files)
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14 #set $name = 'bam_' + str($i) + '.bam'
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15 ln -s '${file}' $name &&
1b690aa060f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass commit 2dc6baaeb2d595cbd8d8ffe3bf22b199a0ba23e4
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16 $bam_filenames.append($name)
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17 #end for
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18 #set $allFiles = ','.join( [ str( $file ) for $file in $bam_filenames ] )
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19 psiclass
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20 -b $allFiles
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21 -p \${GALAXY_SLOTS:-8}
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22 #if $splice_conditional.selector == 'true'
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23 -s '${splice_conditional.splice_file}'
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24 #end if
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25 -c $subexonClassifier
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26 --sa $intronCoverage
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27 --vd $transcriptCoverage
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28 #if $stranded
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29 --stranded $stranded
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30 #end if
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31 --maxDpConstraintSize $maxDpConstraintSize
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32 $primaryParalog
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33 --tssTesQuantile $tssTesQuantile
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34 && mv *sample* "./annotation_files"
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35 #if $splice_conditional.selector == 'false'
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36 && cat ./splice/psiclass_bam.trusted_splice > '${splice_sites}'
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37 #end if
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38 ]]></command>
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39 <inputs>
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40 <param argument="-b" name="bam_files" type="data" format="bam" multiple="true" label="BAM file(s)"
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41 help="PsiCLASS has been tuned to run on alignments generated with the tools HISAT and STAR" />
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42 <conditional name="splice_conditional">
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43 <param name="selector" type="select" label="Provide trusted splice sites coordinates" help="It is possible to supply
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44 an set of trusted introns, for instance generated by RNASTAR or extracted from the GENCODE gene annotations">
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45 <option value="true">Enabled</option>
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46 <option value="false" selected="true">Disabled</option>
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47 </param>
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48 <when value="true">
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49 <param argument="-s" name="splice_file" type="data" format="interval" optional="true" label="Splice junction sites file" help="High confidence collapsed splice junction file" />
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50 </when>
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51 <when value="false"/>
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52 </conditional>
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53 <param argument="-c" type="float" name="subexonClassifier" min="0" max="1" value="0.05" label="Subexon classifier score threshold"
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54 help="Only use the subexons with classifier score minor or equal than the given number" />
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55 <param argument="--sa" name="intronCoverage" type="float" min="0" value="0.5" label="Minimum retained intron converage"
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56 help="Minimum average number of supported read for retained introns" />
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57 <param argument="--vd" name="transcriptCoverage" type="float" min="0" value="1" label="Minimum transcript coverage"
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58 help="Minimum average coverage depth of a transcript to be reported" />
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59 <param argument="--stranded" type="select" optional="true" label="Library strand information" help="Stranded data shows advantages over
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60 non-stranded RNA-Seq data such as higher assembly and differential expression accuracy">
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61 <option value="un">unstranded</option>
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62 <option value="rf">fr-firststrand (rf): first read from the opposite strand.</option>
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63 <option value="fr">fr-secondstrand (fr): first read from the transcript strand</option>
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64 </param>
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65 <param argument="--maxDpConstraintSize" type="integer" min="-1" value="7" label="Constrain cover iN median exon depth (DP)" help="-1 for infinite"/>
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66 <param argument="--primaryParalog" type="boolean" truevalue="--primaryParalog" falsevalue="" checked="false" optional="true"
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67 label="Use primary alignment to retain paralog genes" help="Default: use unique alignments" />
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68 <param argument="--tssTesQuantile" type="float" min="0" max="1" value="0.5" label="Quantile for transcription start/end sites in subexon graph"/>
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69 </inputs>
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70 <outputs>
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71 <data name="meta_anotation" format="gtf" from_work_dir="psiclass_vote.gtf" label="${tool.name} on ${on_string}: meta-annotation" />
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72 <collection name="annotation_collection" type="list" label="${tool.name} on ${on_string}: per-sample annotations">
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73 <discover_datasets pattern="__designation_and_ext__" format="gtf" directory="annotation_files"/>
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74 </collection>
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75 <data name="splice_sites" format="interval" label="${tool.name} on ${on_string}: splice sites">
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76 <filter>splice_conditional["selector"] == "false"</filter>
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77 </data>
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78 </outputs>
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79 <tests>
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80 <test expect_num_outputs="2">
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81 <param name="bam_files" value="reads1.bam,reads2.bam"/>
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82 <param name="subexonClassifier" value="0.05"/>
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83 <param name="intronCoverage" value="0.5"/>
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84 <param name="transcriptCoverage" value="1"/>
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85 <param name="stranded" value="un"/>
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86 <param name="maxDpConstraintSize" value="7"/>
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87 <param name="primaryParalog" value="false"/>
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88 <param name="tssTesQuantile" value="0.5"/>
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89 <conditional name="splice_conditional">
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90 <param name="selector" value="true"/>
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91 <param name="splice_file" value="splice_sites.interval"/>
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92 </conditional>
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93 <output name="meta_anotation" ftype="gtf" file="test01_meta_annotation.gtf" lines_diff="2"/>
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94 <output_collection name="annotation_collection" type="list" count="2">
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95 <element name="psiclass_sample_0" ftype="gtf" file="test01_annotation_sample0.gtf" lines_diff="2"/>
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96 <element name="psiclass_sample_1" ftype="gtf" file="test01_annotation_sample1.gtf" lines_diff="2"/>
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97 </output_collection>
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98 </test>
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99 <test expect_num_outputs="3">
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100 <param name="bam_files" value="reads1.bam,reads2.bam"/>
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101 <param name="subexonClassifier" value="0.05"/>
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102 <param name="intronCoverage" value="0.3"/>
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103 <param name="transcriptCoverage" value="0.5"/>
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104 <param name="stranded" value="rf"/>
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105 <param name="maxDpConstraintSize" value="6"/>
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106 <param name="primaryParalog" value="true"/>
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107 <param name="tssTesQuantile" value="0.4"/>
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108 <conditional name="splice_conditional">
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109 <param name="selector" value="false"/>
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110 </conditional>
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111 <output name="meta_anotation" ftype="gtf" file="test02_meta_annotation.gtf"/>
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112 <output_collection name="annotation_collection" type="list" count="2">
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113 <element name="psiclass_sample_0" ftype="gtf" file="test02_annotation_sample0.gtf" lines_diff="2"/>
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114 <element name="psiclass_sample_1" ftype="gtf" file="test02_annotation_sample1.gtf" lines_diff="2"/>
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115 </output_collection>
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116 <output name="splice_sites" ftype="interval" file="test02_splice_sites.txt"/>
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117 </test>
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118 <test expect_num_outputs="3">
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119 <param name="bam_files" value="reads1.bam"/>
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120 <output name="meta_anotation" ftype="gtf" file="test03_meta_annotation.gtf"/>
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121 <output_collection name="annotation_collection" type="list" count="1">
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122 <element name="psiclass_sample_0" ftype="gtf" file="test03_annotation_sample0.gtf" lines_diff="2"/>
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123 </output_collection>
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124 <output name="splice_sites" file="test03_splice_sites.txt" ftype="interval"/>
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125 </test>
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126 </tests>
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127 <help><![CDATA[
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128
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129 .. class:: infomark
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130
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131 **What is PsiCLASS?**
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132
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133 PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.
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134
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135 Unlike conventional methods that analyze each sample separately and then merge the outcomes to create a unified set of meta-annotations,
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136 PsiCLASS takes a multi-sample approach, simultaneously analyzing all RNA-seq data sets in an experiment.
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137
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138 PsiCLASS is both a transcript assembler and a meta-assembler, producing separate transcript sets for the individual samples and a unified
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139 set of meta-annotations. The algorithmic underpinnings of PsiCLASS include using a global subexon splice graph, statistical cross-sample
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140 feature (intron, subexon) selection methods, and an efficient dynamic programming algorithm to select a subset of transcripts from among
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141 those encoded in the graph, based on the read support in each sample.
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142
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143 Lastly, the set of meta-annotations is selected from among the transcripts generated for individual samples by voting. While PsiCLASS is
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144 highly accurate and efficient for medium-to-large collections of RNA-seq data, its accuracy is equally high for small RNA-seq data sets
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145 (2-10 samples) and is competitive to reference methods for single samples. Additionally, its performance is robust with the aggregation
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146 method used, including the built-in voting and assembly-based approaches such as StringTie-merge and TACO. Therefore, it can be effectively
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147 used as a multi-sample and as a single-sample assembler, as well as in conventional assemble-and-merge protocols.
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148
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149 ]]></help>
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150 <expand macro="citations" />
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151 </tool>