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annotate mircounts.xml @ 12:6d3e98cba73a draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
author artbio
date Sat, 12 May 2018 09:06:24 -0400
parents 7d50d8d0c8c4
children b045c30fb768
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12
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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1 <tool id="mircounts" name="miRcounts" version="1.3.2">
0
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2 <description> Counts miRNA alignments from small RNA sequence data</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.0">bowtie</requirement>
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5 <requirement type="package" version="1.6.0">samtools</requirement>
65befdc9925a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3514091150570410ce32cbdfda26fd6e5591fef1
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6 <requirement type="package" version="0.11.2.2">pysam</requirement>
0
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7 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
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8 <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement>
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9 </requirements>
10
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10 <stdio>
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11 <exit_code range="1:" level="warning" description="Tool exception" />
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12 </stdio>
0
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13 <command detect_errors="exit_code"><![CDATA[
10
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14 tar -xvzf '$__tool_directory__'/mirbase.tar.gz &&
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15 python '$__tool_directory__'/mature_mir_gff_translation.py
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16 --gff_path mirbase/${mirbase_version}/genomes/${genomeKey}.gff3
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17 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
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18 python '$__tool_directory__'/format_fasta_hairpins.py
de227b7307cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
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19 --hairpins_path mirbase/${mirbase_version}/hairpin.fa.gz
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20 --basename ${genomeKey}
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21 --output hairpin.fa &&
0
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22 #if $cutadapt.cutoption == "yes":
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23 python '$__tool_directory__'/yac.py --input $cutadapt.input
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24 --output clipped_input.fastq
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25 --output_format fastq
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26 --adapter_to_clip $cutadapt.clip_source.clip_sequence
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27 --min $cutadapt.min
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28 --max $cutadapt.max
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29 --Nmode $cutadapt.Nmode &&
10
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30 #else:
0
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31 ln -f -s '$cutadapt.clipped_input' clipped_input.fastq &&
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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32 #end if
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33 bowtie-build hairpin.fa hairpin &&
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34 bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -O bam -o '$output' &&
0
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35 samtools index $output &&
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36 python '$__tool_directory__'/mircounts.py --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe
0
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37 #if $plotting.plottingOption == 'yes':
10
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38 && Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF
0
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39 #end if
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40 ]]></command>
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41 <inputs>
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42 <conditional name="cutadapt">
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43 <param label="Remove adapter sequence before aligning" name="cutoption" type="select">
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44 <option value="no">no</option>
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45 <option selected="True" value="yes">yes</option>
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46 </param>
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47 <when value="yes">
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48 <param format="fastq,fastqsanger" label="Source file" name="input" type="data" />
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49 <param label="min size" name="min" size="4" type="integer" value="15" help="Minimum size of accepted clipped reads" />
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50 <param label="max size" name="max" size="4" type="integer" value="36" help="Maximum size of accepted clipped reads"/>
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51 <param label="Accept reads containing N?" name="Nmode" type="select">
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52 <option selected="True" value="accept">accept</option>
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53 <option value="reject">reject</option>
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54 </param>
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55 <conditional name="clip_source">
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56 <param help="Built-in adapters or User-provided" label="Source" name="clip_source_list" type="select">
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57 <option selected="True" value="prebuilt">Use a built-in adapter (select from the list below)</option>
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58 <option value="user">Use custom sequence</option>
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59 </param>
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60 <when value="prebuilt">
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61 <param help="if your adapter is not listed, input your own sequence" label="Select Adapter to clip" name="clip_sequence" type="select">
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62 <option value="TCGTATGCCGTCTTCTGCTTG">Solexa TCGTATGCCGTCTTCTGCTTG</option>
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63 <option value="ATCTCGTATGCCGTCTTCTGCTT">Illumina ATCTCGTATGCCGTCTTCTGCTT</option>
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64 <option selected="True" value="TGGAATTCTCGGGTGCCAAG">Illumina TruSeq TGGAATTCTCGGGTGCCAAG</option>
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65 <option value="CTGTAGGCACCATCAATCGT">IdT CTGTAGGCACCATCAATCGT</option>
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66 </param>
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67 </when>
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68 <when value="user">
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69 <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" />
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70 </when>
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71 </conditional>
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72 </when>
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73 <when value="no">
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74 <param label="Select fastq files to align" name="clipped_input" type="data" format="fastq,fastqsanger" help="Note that sequences reads must be clipped from their adapter" />
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75 </when>
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76 </conditional>
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77 <param name="genomeKey" type="select" label="Choose Organism">
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78 <options from_data_table="miRbase_GenomeKeys">
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79 <column name="name" index="1"/>
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80 <column name="value" index="0"/>
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81 </options>
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82 </param>
4
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83 <param name="mirbase_version" type="select" label="Choose miRbase version">
9
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84 <option selected="true" value="22">22</option>
8
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artbio
parents: 7
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85 <option value="21">21</option>
5
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artbio
parents: 4
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86 <option value="20">20</option>
4
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artbio
parents: 3
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87 <option value="19">19</option>
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artbio
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88 </param>
0
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artbio
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89 <param help="command [ bowtie -v 0,1,2,3 -M 1 --best --strata --norc ] will be used. Specify a value for -v (number of mismatches allowed)" label="Number of mismatches allowed" name="v" type="select">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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90 <option value="0">0</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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91 <option selected="true" value="1">1</option>
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artbio
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92 <option value="2">2</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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93 <option value="3">3</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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94 </param>
6
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artbio
parents: 5
diff changeset
95 <param help="Output mature Mir counts" label="Output mature Mir counts"
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artbio
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96 name="output_mir_counts" type="boolean" falsevalue="0" checked="true" truevalue="1" />
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artbio
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97 <param help="Output pre-Mir counts" label="Output pre-Mir counts"
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artbio
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98 name="output_premir_counts" type="boolean" falsevalue="0" checked="true" truevalue="1" />
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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99 <conditional name="plotting">
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artbio
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100 <param label="Additional miRNA charts" name="plottingOption" type="select">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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101 <option value="no">no</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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102 <option value="yes" selected="True">yes</option>
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103 </param>
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104 <when value="yes">
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artbio
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105 <param label="Display Coverage with absolute number of reads or relatively to the total number of read matching the gene or mir" name="display" type="select">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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106 <option selected="True" value="relative">Relative Coverage</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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107 <option value="absolute">Absolute Coverage</option>
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108 </param>
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109 </when>
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110 <when value="no">
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111 </when>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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112 </conditional>
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113 </inputs>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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114 <outputs>
6
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artbio
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115 <data format="bam" label="BAM alignment" name="output" hidden="true" />
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artbio
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116 <data format="gff3" label="GFF3 generated by miRCounts" name="gff3" hidden="true" />
4
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artbio
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117 <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file">
6
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
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118 <filter>output_premir_counts == True</filter>
4
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
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119 <actions>
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
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120 <action name="column_names" type="metadata" default="Gene,Counts" />
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
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121 </actions>
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
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diff changeset
122 </data>
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
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123 <data format="tabular" label="Mir Counts" name="mir_count_file">
6
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
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124 <filter>output_mir_counts == True</filter>
4
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
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125 <actions>
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
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126 <action name="column_names" type="metadata" default="Gene,Counts" />
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artbio
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127 </actions>
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artbio
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diff changeset
128 </data>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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129 <data format="tabular" label="Coverage Table" name="coverage_dataframe">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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130 <filter>plotting['plottingOption'] == "yes"</filter>
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131 </data>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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132 <data format="pdf" label="Pre-mir coverage (${plotting.display})" name="latticePDF">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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133 <filter>plotting['plottingOption'] == "yes"</filter>
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134 </data>
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artbio
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135 </outputs>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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136 <tests>
9
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137 <test>
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artbio
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diff changeset
138 <param name="cutoption" value="yes" />
12
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artbio
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diff changeset
139 <param name="min" value="18"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
140 <param name="max" value="32"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
141 <param name="Nmode" value="reject"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
142 <param name="clip_sequence" value="TGGAATTCTCGGGTGCCAAG"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
143 <param name="v" value="1"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
144 <param name="genomeKey" value="mmu"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
145 <param name="mirbase_version" value="19"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
146 <param name="input" value="mouse.fastq" ftype="fastqsanger"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
147 <param name="plottingOption" value="yes"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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148 <param name="display" value="relative"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
149 <param name="output_premir_counts" value="True"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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150 <param name="output_mir_counts" value="True"/>
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artbio
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diff changeset
151 <output name="output" file="mouse.bam"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
152 <output name="gff3" file="mouse.19.gff3" lines_diff="22"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
153 <output name="pre_mir_count_file" file="mouse_pre_mirs_count.29.tab"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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154 <output name="mir_count_file" file="mouse_mirs_count.29.tab"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
155 <output name="latticePDF" file="mouse_mir_coverage.pdf"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
156 <output name="coverage_dataframe" file="mouse_lattice_dataframe.tab"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
157 </test>
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artbio
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diff changeset
158 <test>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
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diff changeset
159 <param name="cutoption" value="yes" />
9
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artbio
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diff changeset
160 <param name="min" value="15"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
161 <param name="max" value="25"/>
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artbio
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diff changeset
162 <param name="Nmode" value="reject"/>
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artbio
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diff changeset
163 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
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artbio
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diff changeset
164 <param name="v" value="0"/>
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artbio
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diff changeset
165 <param name="genomeKey" value="dme"/>
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artbio
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diff changeset
166 <param name="mirbase_version" value="22"/>
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artbio
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diff changeset
167 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
168 <param name="plottingOption" value="no"/>
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artbio
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diff changeset
169 <param name="output_premir_counts" value="True"/>
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artbio
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170 <param name="output_mir_counts" value="True"/>
10
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171 <output name="output" file="unclipped.out.22.bam"/>
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172 <output name="gff3" file="translated_dme.22.gff3" lines_diff="22"/>
9
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173 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.22.tab"/>
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174 <output name="mir_count_file" file="mirs_unclipped_count.22.tab"/>
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175 </test>
0
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176 <test>
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177 <param name="cutoption" value="yes" />
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178 <param name="min" value="15"/>
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179 <param name="max" value="25"/>
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180 <param name="Nmode" value="reject"/>
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181 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
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182 <param name="v" value="0"/>
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183 <param name="genomeKey" value="dme"/>
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184 <param name="mirbase_version" value="21"/>
0
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185 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/>
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186 <param name="plottingOption" value="no"/>
6
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187 <param name="output_premir_counts" value="True"/>
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188 <param name="output_mir_counts" value="True"/>
10
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189 <output name="output" file="unclipped.out.bam" />
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190 <output name="gff3" file="translated_dme.gff3" lines_diff="22"/>
0
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191 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
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192 <output name="mir_count_file" file="mirs_unclipped_count.tab"/>
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193 </test>
9
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194 <test>
0
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195 <param name="cutoption" value="yes" />
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196 <param name="min" value="15"/>
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197 <param name="max" value="25"/>
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198 <param name="Nmode" value="reject"/>
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199 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
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200 <param name="v" value="0"/>
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201 <param name="genomeKey" value="dme"/>
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202 <param name="mirbase_version" value="21"/>
0
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203 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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204 <param name="plottingOption" value="yes"/>
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205 <param name="display" value="relative"/>
6
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206 <param name="output_premir_counts" value="True"/>
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207 <param name="output_mir_counts" value="True"/>
10
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208 <output name="output" file="unclipped.out.bam"/>
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209 <output name="gff3" file="translated_dme.gff3" lines_diff="22"/>
0
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210 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
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211 <output name="mir_count_file" file="mirs_unclipped_count.tab"/>
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212 <output name="latticePDF" file="mir_unclipped_coverage.pdf"/>
0
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213 <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab"/>
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214 </test>
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215 <test>
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216 <param name="cutoption" value="no" />
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217 <param name="v" value="1"/>
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218 <param name="genomeKey" value="dme"/>
8
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219 <param name="mirbase_version" value="21"/>
0
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220 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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221 <param name="plottingOption" value="yes"/>
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222 <param name="display" value="absolute"/>
6
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223 <param name="output_premir_counts" value="True"/>
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224 <param name="output_mir_counts" value="True"/>
10
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225 <output name="output" file="clipped.out.bam"/>
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226 <output name="gff3" file="translated_dme.gff3" lines_diff="22"/>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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227 <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/>
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228 <output name="mir_count_file" file="mirs_clipped_count.tab"/>
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229 <output name="latticePDF" file="mir_clipped_coverage.pdf"/>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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230 <output name="coverage_dataframe" file="lattice_clipped_dataframe.tab"/>
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231 </test>
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232 </tests>
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233 <help>
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234
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235 **What it does**
1
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236
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237 + Clips adapter (optional)
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238 + Aligns small RNA reads to miRNA mirBase_ reference using bowtie
cadc0f2c6b29 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
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239 + Computes pre-mir and mir counts using the pysam python package
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240 + Plots pre-mir read coverages using R lattice package (optional)
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241
0
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242 This tool uses a species-specific GFF3 file generated from mirBase_ to guide the parsing of a bam file of small RNA alignments.
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243
8
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244 .. _mirBase: ftp://mirbase.org/pub/mirbase/
0
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245
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246 ------
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247
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248
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249 **Inputs**
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250
1
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251 1. A fastq file of reads that may or may not be clipped from their adapter sequence. The tool includes a clipping option if needed.
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252 2. Select the appropriate organism which reads originate from.
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253 3. Choose whether you wish or not to plot the pre-mir coverages. The coverage can be expressed in absolute number of reads covering the real coordinates of the pre-mir sequences, or, as a fraction of the maximum coverage (set to 1) covering the coordinates of pre-mirs expressed as a fraction of the length of the pre-mirs.
0
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254
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255
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256 ------
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257
1
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258 Absolute :
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259
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260 + .. image:: premirs_absolute.png
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261
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262 Relative :
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263
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264 + .. image:: premirs_relative.png
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265
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266 -------
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267
0
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268 **Outputs**
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269
1
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270 1. A BAM alignment of input reads
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271 2. A GFF3 file generated by the tool to compute mature mir counts
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272 3. A table of pre-mir counts
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273 4. A table of mature mir counts
0
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274
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275 Optional:
1
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276
0
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277 5. A table of pre-mir coverage
1
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278 6. A PDF file with covererage plots
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279
0
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280
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281 </help>
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282 <citations>
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283 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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284 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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285 <citation type="bibtex">@Book{,
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286 title = {Lattice: Multivariate Data Visualization with R},
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287 author = {Deepayan Sarkar},
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288 publisher = {Springer},
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289 address = {New York},
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290 year = {2008},
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291 note = {ISBN 978-0-387-75968-5},
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292 url = {http://lmdvr.r-forge.r-project.org},
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293 }</citation>
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294 </citations>
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295 </tool>