Mercurial > repos > iuc > ucsc_maftoaxt

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt commit 303002db06287fb25306020c4391626842f52162
author iuc
date Sun, 22 Sep 2024 07:24:57 +0000
parents d1f6d417813d
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1 <tool id="maftoaxt" name="mafToAxt" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
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2 <description>
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3 Convert file from MAF to axt format
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4 </description>
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5 <macros>
1
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6 <token name="@TOOL_VERSION@">469</token>
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7 </macros>
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8 <xrefs>
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9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
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10 </xrefs>
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">ucsc-maftoaxt</requirement>
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13 </requirements>
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14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
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15 <command detect_errors="exit_code"><![CDATA[
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16 mafToAxt
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17 '$in_maf'
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18 #if $tar_seq.tarSeq == "customTar"
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19 '$tar_seq.targetSeq'
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20 #else
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21 first
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22 #end if
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23 '$querySeq'
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24 '$out'
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25 $stripDb
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26 ]]></command>
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27 <inputs>
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28 <param name="in_maf" format="maf" type="data" label="MAF dataset" />
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29
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30 <conditional name="tar_seq">
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31 <param name="tarSeq" type="select" label="Select target sequence" optional="false" help="Which sequence from the MAF file should be used as the target sequence. ">
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32 <option value="" selected="true">Use the first sequence of the block as the target</option>
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33 <option value="customTar">Specify the target sequence by name</option>
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34 </param>
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35 <when value="customTar">
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36 <param optional="false" name="targetSeq" type="text" label="Name of sequence that should be used as target sequence" help="Must be present in the MAF file." />
d1f6d417813d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/maftoaxt commit f12613ba8034a78d45054ec07a7cd6853dbb62aa
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37 </when>
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38 <when value="" />
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39 </conditional>
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40
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41 <param name="querySeq" type="text" optional="false" label="Name of sequence that should be used as the query sequence" help="Must be present in the MAF file." />
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42 <param argument="-stripDb" type="boolean" truevalue="-stripDb" falsevalue="" label="Strip names from start to the first period" help="'hg38.chr19' becomes 'chr19'" />
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43
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44 </inputs>
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45 <outputs>
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46 <data name="out" format="axt" />
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="in_maf" value="1.maf"/>
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51 <param name="querySeq" value="panTro1"/>
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52 <output name="out" file="1.axt"/>
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53 </test>
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54 <test>
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55 <param name="in_maf" value="1.maf"/>
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56 <param name="tarSeq" value="customTar"/>
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57 <param name="targetSeq" value="panTro1"/>
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58 <param name="querySeq" value="rn3"/>
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59 <output name="out" file="2.axt"/>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 **What it does**
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64
1
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65 `mafToAxt`_ is a tool to convert `MAF`_ dataset to `axt`_ format. Depending on parameters and the number of alignments in the MAF file this can be a full conversion or data extraction.
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66
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67 For implementation details see mafToAxt's `source code`_.
0
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68
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69 .. _mafToAxt: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
1
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70 .. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html
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71 .. _MAF: https://genome.ucsc.edu/FAQ/FAQformat.html#format5
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72 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/mafToAxt/mafToAxt.c
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73 ]]> </help>
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74 <citations>
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75 <citation type="doi">10.1093/bib/bbs038</citation>
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76 </citations>
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77 </tool>