Mercurial > repos > iuc > ucsc_maffrag

annotate mafFrag.xml @ 0:e452e9e359e7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
author iuc
date Tue, 09 Sep 2025 16:20:32 +0000
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0
e452e9e359e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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1 <tool id="ucsc_maffrag" name="mafFrag" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>Extract MAF sequences for a region from database</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">482</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <token name="@PROFILE@">24.2</token>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">ucsc-maffrag</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13 cp '$ucsc_db_connection' "\${HOME}/.hg.conf" &&
e452e9e359e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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14 chmod 600 "\${HOME}/.hg.conf" &&
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15 mafFrag '$genome' '$track' '$chrom' '$start' '$end' '$strand' out.maf
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16 ]]>
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17 </command>
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18 <configfiles>
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19 <configfile name="ucsc_db_connection"><![CDATA[
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20 #European MariaDB server
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21 db.host=genome-euro-mysql.soe.ucsc.edu
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22 db.user=genomep
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23 db.password=password
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24 central.db=hgcentral
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25 central.host=genome-euro-mysql.soe.ucsc.edu
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26 central.user=genomep
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27 central.password=password
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28 gbdbLoc1=http://hgdownload.soe.ucsc.edu/gbdb/
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29 forceTwoBit=on
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30 ]]></configfile>
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31 </configfiles>
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32 <inputs>
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33 <param name="genome" type="text" optional="false" label="Enter Genome database name" help="Name should match with the UCSC Table Browser Entries (For Eg. mm10, hg19, hg38)"/>
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34 <param name="track" type="text" optional="false" label="Enter UCSC Table name for desired table of the above genome" help="Table name should match with the UCSC Table Browser Entries (For eg. knownGene, all_mrna)"/>
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35 <param name="chrom" type="text" optional="false" label="Chromosome" help="Chromosome name (e.g., chr1, chr2, etc.)"/>
e452e9e359e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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36 <param name="start" type="integer" optional="false" label="Start position" help="Start position of the region in the chromosome (0-based)"/>
e452e9e359e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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37 <param name="end" type="integer" optional="false" label="End position" help="End position of the region in the chromosome (0-based)"/>
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38 <param name="strand" type="select" optional="false" label="Strand" help="Strand of the region">
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39 <option value=".">No Strand</option>
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40 <option value="+">Forward Strand(+)</option>
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41 <option value="-">Reverse Strand(-)</option>
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42 </param>
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43 </inputs>
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44 <outputs>
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45 <data name="output" format="maf" from_work_dir="out.maf" label="${tool.name} on ${on_string}:Output MAF"/>
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46 </outputs>
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47 <tests>
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48 <!-- Test 01: Testing with default options -->
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49 <test expect_num_outputs="1">
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50 <param name="genome" value="hg19"/>
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51 <param name="track" value="multiz46way"/>
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52 <param name="chrom" value="chr17"/>
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53 <param name="start" value="7578370"/>
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54 <param name="end" value="7578400"/>
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55 <param name="strand" value="+"/>
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56 <output name="output" ftype="maf">
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57 <assert_contents>
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58 <has_n_lines n="43"/>
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59 <has_size value="3087"/>
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60 <has_line line="s hg19.chr17 7578370 30 + 81195210 CA---TCGCTA----TCTGAG--CAGCGCTC-ATGGTGGG"/>
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61 </assert_contents>
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62 </output>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66
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67 mafFrag is a command-line tool from the UCSC Genome Browser suite that extracts MAF sequences for a region from database.
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68
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69 ]]></help>
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70 <citations>
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71 <citation type="bibtex">
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72 @misc{mafFrag,
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73 author = {Kent UCSC},
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74 title = {mafFrag: A tool that extracts MAF sequences for a region from database},
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75 note = {Tool that extracts MAF sequences for a region from database}
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76 </citation>
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77 </citations>
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78 <creator>
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79 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12" identifier="https://orcid.org/0009-0003-9935-828X"/>
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80 <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
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81 </creator>
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iuc
parents:
diff changeset
82 </tool>