Mercurial > repos > dave > genebed_maf_to_fasta

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
author dave
date Fri, 24 Jul 2020 13:03:33 -0400
parents be26293ade92
children
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be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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1 <tool id="GeneBed_Maf_Fasta2" name="Stitch Gene blocks" version="1.0.1">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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2 <description>given a set of coding exon intervals</description>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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3 <macros>
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4 <import>macros.xml</import>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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5 </macros>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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6 <command>
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7 <![CDATA[
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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8 #if $maf_source_type.maf_source == "cached"
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9 #set $tab = '\t'
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10 echo "$maf_source_type.mafType.fields.name${tab}$maf_source_type.mafType.fields.value${tab}$maf_source_type.mafType.fields.indexed_for${tab}$maf_source_type.mafType.fields.exists_in_maf${tab}$maf_source_type.mafType.fields.path" >> ./maf_indexes.loc &&
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11 #end if
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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12
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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13 python '$__tool_directory__/interval_maf_to_merged_fasta.py'
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14 #if $maf_source_type.maf_source == "user"
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15 --mafSource='$maf_source_type.mafFile' --mafIndex='$maf_source_type.mafFile.metadata.maf_index'
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16 #else
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17 --mafSource=./maf_indexes.loc
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18 #end if
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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19 --geneBED
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20 --dbkey=$dbkey
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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21 --species=$maf_source_type.species
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22 --interval_file='$input1'
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23 --output_file='$out_file1'
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24 --mafSourceType=$maf_source_type.maf_source
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25 --mafIndexFileDir=.
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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26 --overwrite_with_gaps=$overwrite_with_gaps
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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27 ]]>
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28 </command>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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29 <inputs>
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30 <param name="input1" type="data" format="bed" label="Gene BED File">
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31 <validator type="unspecified_build" />
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32 <validator type="expression" message="Input must be in BED12 format.">value.metadata.columns &gt;= 12</validator> <!-- allow 12+ columns, not as strict as possible. TODO: only list bed files with 12+ columns -->
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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33 </param>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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34 <expand macro="maf_source" />
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35 <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occurring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block.">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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36 <option value="True" selected="true">No</option>
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37 <option value="False">Yes</option>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data format="fasta" name="out_file1" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input1" dbkey="hg38" value="maf_to_fasta-in1.bed"/>
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46 <param name="maf_source" value="cached"/>
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47 <param name="maf_identifier" value="test"/>
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48 <param name="species" value="hg38,eulFla1,mm10"/>
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49 <param name="overwrite_with_gaps" value="True"/>
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50 <output name="out_file1" file="maf_to_fasta-out1.fasta" />
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51 </test>
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52 <test>
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53 <param name="input1" dbkey="hg38" value="maf_to_fasta-in2.bed"/>
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54 <param name="maf_source" value="user"/>
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55 <param name="maf_file" dbkey="hg38" value="maf_to_fasta-in2.maf"/>
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56 <param name="species" value="hg38,eulFla1,mm10"/>
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57 <param name="overwrite_with_gaps" value="True"/>
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58 <output name="out_file1" file="maf_to_fasta-out2.fasta" />
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59 </test>
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60 </tests>
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61 <help>
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62 **What it does**
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63
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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64 The coding sequence of genes are usually composed of several coding exons. Each of these coding exons is an individual genomic region, which when concatenated with each other constitutes the coding sequence. A single genomic region can be covered by multiple alignment blocks. In many cases it is desirable to stitch these alignment blocks together. This tool accepts a list of gene-based intervals, in the Gene BED format. For every interval it performs the following:
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65
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66 * finds all MAF blocks that overlap the coding regions;
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67 * sorts MAF blocks by alignment score;
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68 * stitches blocks together and resolves overlaps based on alignment score;
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69 * outputs alignments in FASTA format.
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70 </help>
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71 <expand macro="citations" />
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72 </tool>