annotate mircounts.xml @ 13:b045c30fb768 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
author artbio
date Fri, 18 Oct 2019 19:18:50 -0400
parents 6d3e98cba73a
children c163574c246f
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1 <tool id="mircounts" name="miRcounts" version="1.4.0">
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="1.9=h10a08f8_12">samtools</requirement>
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6 <requirement type="package" version="0.15.3=py27hda2845c_1">pysam</requirement>
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7 <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
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8 <requirement type="package" version="0.20_38=r36hcdcec82_1002">r-lattice</requirement>
0
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9 </requirements>
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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[
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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
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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 $cutadapt.Nmode &&
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30 #else:
0
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31 ln -f -s '$cutadapt.clipped_input' clipped_input.fastq &&
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32 #end if
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33 bowtie-build hairpin.fa hairpin &&
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34 bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '$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 $plotting.plottingOption == 'yes':
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38 && Rscript '$__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">
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84 <option selected="true" value="22">22</option>
8
3f62272192f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 0eaefbad21786cabed6791a6d06e9a0de8af10b0
artbio
parents: 7
diff changeset
85 <option value="21">21</option>
5
9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
artbio
parents: 4
diff changeset
86 <option value="20">20</option>
4
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
parents: 3
diff changeset
87 <option value="19">19</option>
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
parents: 3
diff changeset
88 </param>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
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
parents:
diff changeset
90 <option value="0">0</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
91 <option selected="true" value="1">1</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
92 <option value="2">2</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
93 <option value="3">3</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
94 </param>
6
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
parents: 5
diff changeset
95 <param help="Output mature Mir counts" label="Output mature Mir counts"
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
parents: 5
diff changeset
96 name="output_mir_counts" type="boolean" falsevalue="0" checked="true" truevalue="1" />
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
parents: 5
diff changeset
97 <param help="Output pre-Mir counts" label="Output pre-Mir counts"
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
parents: 5
diff changeset
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
artbio
parents:
diff changeset
99 <conditional name="plotting">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
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
parents:
diff changeset
101 <option value="no">no</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
102 <option value="yes" selected="True">yes</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
103 </param>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
104 <when value="yes">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
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
artbio
parents:
diff changeset
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
parents:
diff changeset
107 <option value="absolute">Absolute Coverage</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
108 </param>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
109 </when>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
110 <when value="no">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
111 </when>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
112 </conditional>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
113 </inputs>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
114 <outputs>
6
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
parents: 5
diff changeset
115 <data format="bam" label="BAM alignment" name="output" hidden="true" />
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
parents: 5
diff changeset
116 <data format="gff3" label="GFF3 generated by miRCounts" name="gff3" hidden="true" />
4
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
parents: 3
diff changeset
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
artbio
parents: 5
diff changeset
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
parents: 3
diff changeset
119 <actions>
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
parents: 3
diff changeset
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
artbio
parents: 3
diff changeset
121 </actions>
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
parents: 3
diff changeset
122 </data>
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
parents: 3
diff changeset
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
artbio
parents: 5
diff changeset
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
parents: 3
diff changeset
125 <actions>
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
parents: 3
diff changeset
126 <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
artbio
parents: 3
diff changeset
127 </actions>
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
parents: 3
diff changeset
128 </data>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
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
parents:
diff changeset
130 <filter>plotting['plottingOption'] == "yes"</filter>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
131 </data>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
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
parents:
diff changeset
133 <filter>plotting['plottingOption'] == "yes"</filter>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
134 </data>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
135 </outputs>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
136 <tests>
9
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents: 8
diff changeset
137 <test>
13
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
138 <param name="cutoption" value="no" />
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
139 <param name="v" value="1"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
140 <param name="genomeKey" value="aga"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
141 <param name="mirbase_version" value="22"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
142 <param name="clipped_input" value="aga.fastqsanger" ftype="fastqsanger"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
143 <param name="plottingOption" value="yes"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
144 <param name="display" value="relative"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
145 <param name="output_premir_counts" value="True"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
146 <param name="output_mir_counts" value="True"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
147 <output name="output" file="aga.bam"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
148 <output name="gff3" file="aga.22.gff3" lines_diff="22"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
149 <output name="pre_mir_count_file" file="aga_pre_mirs_count.22.tab"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
150 <output name="mir_count_file" file="aga_mirs_count.22.tab"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
151 <output name="latticePDF" file="aga_mir_coverage.pdf"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
152 <output name="coverage_dataframe" file="aga_lattice_dataframe.tab"/>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
153 </test>
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents: 12
diff changeset
154 <test>
9
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents: 8
diff changeset
155 <param name="cutoption" value="yes" />
12
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
parents: 11
diff changeset
156 <param name="min" value="18"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
parents: 11
diff changeset
157 <param name="max" value="32"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
parents: 11
diff changeset
158 <param name="Nmode" value="reject"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
parents: 11
diff changeset
159 <param name="clip_sequence" value="TGGAATTCTCGGGTGCCAAG"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
parents: 11
diff changeset
160 <param name="v" value="1"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
parents: 11
diff changeset
161 <param name="genomeKey" value="mmu"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
parents: 11
diff changeset
162 <param name="mirbase_version" value="19"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
parents: 11
diff changeset
163 <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
parents: 11
diff changeset
164 <param name="plottingOption" value="yes"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
parents: 11
diff changeset
165 <param name="display" value="relative"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
parents: 11
diff changeset
166 <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
parents: 11
diff changeset
167 <param name="output_mir_counts" value="True"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
parents: 11
diff changeset
168 <output name="output" file="mouse.bam"/>
6d3e98cba73a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
artbio
parents: 11
diff changeset
169 <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
parents: 11
diff changeset
170 <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
parents: 11
diff changeset
171 <output name="mir_count_file" file="mouse_mirs_count.29.tab"/>
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artbio
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diff changeset
172 <output name="latticePDF" file="mouse_mir_coverage.pdf"/>
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artbio
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173 <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
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174 </test>
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175 <test>
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176 <param name="cutoption" value="yes" />
9
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artbio
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177 <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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178 <param name="max" value="25"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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179 <param name="Nmode" value="reject"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
180 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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181 <param name="v" value="0"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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182 <param name="genomeKey" value="dme"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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183 <param name="mirbase_version" value="22"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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184 <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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185 <param name="plottingOption" value="no"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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186 <param name="output_premir_counts" value="True"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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187 <param name="output_mir_counts" value="True"/>
10
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artbio
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188 <output name="output" file="unclipped.out.22.bam"/>
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artbio
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189 <output name="gff3" file="translated_dme.22.gff3" lines_diff="22"/>
9
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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190 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.22.tab"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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191 <output name="mir_count_file" file="mirs_unclipped_count.22.tab"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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192 </test>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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193 <test>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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194 <param name="cutoption" value="yes" />
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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195 <param name="min" value="15"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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196 <param name="max" value="25"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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197 <param name="Nmode" value="reject"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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198 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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199 <param name="v" value="0"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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200 <param name="genomeKey" value="dme"/>
8
3f62272192f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 0eaefbad21786cabed6791a6d06e9a0de8af10b0
artbio
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201 <param name="mirbase_version" value="21"/>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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202 <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
artbio
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203 <param name="plottingOption" value="no"/>
6
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
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204 <param name="output_premir_counts" value="True"/>
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
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205 <param name="output_mir_counts" value="True"/>
10
de227b7307cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
artbio
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206 <output name="output" file="unclipped.out.bam" />
de227b7307cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
artbio
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207 <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
artbio
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208 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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209 <output name="mir_count_file" file="mirs_unclipped_count.tab"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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210 </test>
9
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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211 <test>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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212 <param name="cutoption" value="yes" />
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artbio
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213 <param name="min" value="15"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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214 <param name="max" value="25"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
215 <param name="Nmode" value="reject"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
216 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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217 <param name="v" value="0"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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218 <param name="genomeKey" value="dme"/>
8
3f62272192f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 0eaefbad21786cabed6791a6d06e9a0de8af10b0
artbio
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diff changeset
219 <param name="mirbase_version" value="21"/>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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220 <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
artbio
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221 <param name="plottingOption" value="yes"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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222 <param name="display" value="relative"/>
6
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
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223 <param name="output_premir_counts" value="True"/>
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
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224 <param name="output_mir_counts" value="True"/>
10
de227b7307cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
artbio
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225 <output name="output" file="unclipped.out.bam"/>
de227b7307cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
artbio
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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
artbio
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227 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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228 <output name="mir_count_file" file="mirs_unclipped_count.tab"/>
10
de227b7307cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
artbio
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229 <output name="latticePDF" file="mir_unclipped_coverage.pdf"/>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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230 <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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231 </test>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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232 <test>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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233 <param name="cutoption" value="no" />
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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234 <param name="v" value="1"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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235 <param name="genomeKey" value="dme"/>
8
3f62272192f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 0eaefbad21786cabed6791a6d06e9a0de8af10b0
artbio
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diff changeset
236 <param name="mirbase_version" value="21"/>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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237 <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
artbio
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238 <param name="plottingOption" value="yes"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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239 <param name="display" value="absolute"/>
6
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
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diff changeset
240 <param name="output_premir_counts" value="True"/>
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
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241 <param name="output_mir_counts" value="True"/>
10
de227b7307cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
artbio
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diff changeset
242 <output name="output" file="clipped.out.bam"/>
de227b7307cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
artbio
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diff changeset
243 <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
artbio
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244 <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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245 <output name="mir_count_file" file="mirs_clipped_count.tab"/>
10
de227b7307cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
artbio
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diff changeset
246 <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
artbio
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247 <output name="coverage_dataframe" file="lattice_clipped_dataframe.tab"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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248 </test>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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249 </tests>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
250 <help>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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251
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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252 **What it does**
1
cadc0f2c6b29 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
artbio
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253
cadc0f2c6b29 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
artbio
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254 + Clips adapter (optional)
cadc0f2c6b29 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
artbio
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diff changeset
255 + 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
artbio
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256 + Computes pre-mir and mir counts using the pysam python package
cadc0f2c6b29 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
artbio
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257 + Plots pre-mir read coverages using R lattice package (optional)
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258
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259 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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260
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261 .. _mirBase: ftp://mirbase.org/pub/mirbase/
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262
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263 ------
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264
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265
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266 **Inputs**
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267
1
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268 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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269 2. Select the appropriate organism which reads originate from.
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270 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.
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271
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273 ------
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274
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275 Absolute :
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276
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277 + .. image:: premirs_absolute.png
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278
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279 Relative :
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280
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281 + .. image:: premirs_relative.png
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282
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283 -------
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284
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285 **Outputs**
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286
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287 1. A BAM alignment of input reads
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288 2. A GFF3 file generated by the tool to compute mature mir counts
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289 3. A table of pre-mir counts
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290 4. A table of mature mir counts
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291
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292 Optional:
1
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293
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294 5. A table of pre-mir coverage
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295 6. A PDF file with covererage plots
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296
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297
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298 </help>
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299 <citations>
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300 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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301 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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302 <citation type="bibtex">@Book{,
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303 title = {Lattice: Multivariate Data Visualization with R},
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304 author = {Deepayan Sarkar},
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305 publisher = {Springer},
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306 address = {New York},
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307 year = {2008},
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308 note = {ISBN 978-0-387-75968-5},
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309 url = {http://lmdvr.r-forge.r-project.org},
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310 }</citation>
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311 </citations>
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312 </tool>