Mercurial > repos > drosofff > msp_sr_signature
annotate signature.xml @ 1:6218b518cd16 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
author | drosofff |
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date | Wed, 07 Jun 2017 17:53:44 -0400 |
parents | a2f293717ce3 |
children | 229645380cb9 |
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6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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1 <tool id="signature" name="Small RNA Signatures" version="2.1.0"> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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2 <description /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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3 <requirements> |
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6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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4 <requirement type="package" version="1.1.2">bowtie</requirement> |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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5 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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6 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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7 <!-- <requirement type="package" version="3.1.2">R</requirement> --> |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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8 <requirement type="package" version="0.20_33=r3.2.2_0a">r-lattice</requirement> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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9 </requirements> |
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6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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10 <command><![CDATA[ |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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11 python '$__tool_directory__'/signature.py |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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12 --input '$refGenomeSource.input' |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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13 --inputFormat '$refGenomeSource.input.ext' |
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a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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14 --minquery $minquery |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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15 --maxquery $maxquery |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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16 --mintarget $mintarget |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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17 --maxtarget $maxtarget |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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18 --minscope $minscope |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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19 --maxscope $maxscope |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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20 --outputOverlapDataframe $output |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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21 #if $refGenomeSource.genomeSource == "history": |
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6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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22 --referenceGenome '$refGenomeSource.ownFile' |
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a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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23 #else: |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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24 #silent reference= filter( lambda x: str( x[0] ) == str( $input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] |
1
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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25 --referenceGenome '$reference' |
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a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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26 --extract_index |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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27 #end if |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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28 --graph $graph_type |
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6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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29 --rcode '$sigplotter' |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
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30 ]]></command> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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31 <inputs> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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32 <conditional name="refGenomeSource"> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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33 <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select"> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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34 <option value="indexed">Use a built-in index</option> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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35 <option value="history">Use one from the history</option> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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36 </param> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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37 <when value="indexed"> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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38 <param format="tabular,sam,bam" label="Compute signature from this bowtie standard output" name="input" type="data"> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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39 <validator message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history." metadata_column="0" metadata_name="dbkey" table_name="bowtie_indexes" type="dataset_metadata_in_data_table" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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40 </param> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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41 </when> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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42 <when value="history"> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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43 <param format="fasta" label="Select the fasta reference" name="ownFile" type="data" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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44 <param format="tabular,sam,bam" label="Compute signature from this bowtie standard output" name="input" type="data" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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45 </when> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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46 </conditional> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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47 <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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48 <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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49 <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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50 <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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51 <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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52 <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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53 <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="graph_type" type="select"> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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54 <option selected="True" value="global">Global</option> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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55 <option value="lattice">Lattice</option> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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56 </param> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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57 </inputs> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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58 <outputs> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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59 <data format="tabular" label="signature data frame" name="output" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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60 <data format="pdf" label="Overlap probabilities" name="output2" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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61 </outputs> |
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62 <tests> |
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63 <test> |
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64 <param name="genomeSource" value="history" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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65 <param ftype="fasta" name="ownFile" value="ensembl.fa" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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66 <param ftype="bam" name="input" value="sr_bowtie.bam" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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67 <param name="minquery" value="23" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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68 <param name="maxquery" value="29" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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69 <param name="mintarget" value="23" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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70 <param name="maxtarget" value="29" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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71 <param name="minscope" value="5" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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72 <param name="maxscope" value="15" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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73 <param name="graph_type" value="global" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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74 <output file="signature.tab" ftype="tabular" name="output" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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75 <output file="signature.pdf" ftype="pdf" name="output2" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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76 </test> |
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77 </tests> |
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78 <help> |
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79 |
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80 **What it does** |
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81 |
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82 This tool computes the number of pairs by overlap classes (in nt) from a bowtie output file, the z-score calculated from these numbers of pairs, and the ping-pong signal as described in Brennecke et al (2009) Science. |
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83 The numerical options set the min and max size of both the query small rna class and the target small rna class. |
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84 Three type of signals are plotted in separate pdf files, the number of pairs founds, the z-score calculated from these numbers of pairs, and the ping-pong signal as described in Brennecke et al (2009) Science. |
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85 |
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86 </help> |
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87 <citations> |
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88 <citation type="doi">10.1007/978-1-4939-0931-5_12</citation> |
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89 </citations> |
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90 <configfiles> |
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91 <configfile name="sigplotter"> |
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92 graph_type = "${graph_type}" |
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93 |
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94 globalgraph = function () { |
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95 ## Setup R error handling to go to stderr |
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96 options( show.error.messages=F, |
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97 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
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98 signature = read.delim("${output}", header=TRUE) |
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99 signaturez=data.frame(signature[,1], (signature[,2] -mean(signature[,2]))/sd(signature[,2])) |
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100 overlap_prob_z=data.frame(signature[,1], (signature[,3] -mean(signature[,3]))/sd(signature[,3])) |
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101 YLIM=max(signature[,2]) |
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102 |
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103 |
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104 ## Open output2 PDF file |
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105 pdf( "${output2}" ) |
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106 if (YLIM!=0) { |
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107 par(mfrow=c(2,2),oma = c(0, 0, 3, 0)) |
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108 |
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109 plot(signature[,1:2], type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)", ylim=c(0,YLIM), ylab="Numbers of pairs", col="darkslateblue", lwd=4) |
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110 |
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111 plot(signaturez, type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) |
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112 |
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113 plot(signature[,1], signature[,3]*100, type = "l", main="Overlap probabilities", |
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114 cex.main=1, xlab="overlap (nt)", ylab="Probability [%]", ylim=c(0,50), |
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115 pch=19, col="darkslateblue", lwd=2) |
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116 |
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117 plot(overlap_prob_z, type = "l", main="Overlap Probability Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) |
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118 |
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119 mtext("Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", outer = TRUE, cex=1) |
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120 } |
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121 devname = dev.off() |
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122 ## Close the PDF file |
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123 } |
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124 |
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125 treillisgraph = function () { |
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126 ## Open output2 PDF file |
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127 pdf( "${output2}", paper="special", height=11.69, width=8.2677 ) |
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128 signature = read.delim("${output}", header=TRUE) |
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129 options( show.error.messages=F, |
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130 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
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131 library(lattice) |
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132 print (xyplot(signature[,3]*100~signature[,1]|signature[,4], type = "l", xlim=c(${minscope},${maxscope}), main="ping-pong Signature of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", |
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133 par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), scales=list(cex=0.5), |
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134 cex.main=1, cex=.5, xlab="overlap (nt)", ylab="ping-pong signal [%]", |
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135 pch=19, col="darkslateblue", lwd =1.5, cex.lab=1.2, cex.axis=1.2, |
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136 layout=c(4,12), as.table=TRUE, newpage = T) ) |
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137 devnname = dev.off() |
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138 } |
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139 |
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140 if (graph_type=="global") { |
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141 globalgraph() |
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142 |
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143 } |
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144 if(graph_type=="lattice") { |
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145 treillisgraph() |
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146 } |
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147 </configfile> |
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148 </configfiles> |
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149 </tool> |