Mercurial > repos > iuc > ucsc_maffetch

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit fe43201294560762b7aab73785df2f1f7828cb9e
author iuc
date Thu, 14 Aug 2025 11:59:08 +0000
parents eb31f147bf4a
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eb31f147bf4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit b4d87499a5677fbf611eedfa06c1b3d5cdc23914
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1 <tool id="ucsc_maffetch" name="mafFetch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>Get overlapping records from an MAF using an index table</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-maffetch</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 '$ucsc_db_connection' "\${HOME}/.hg.conf" &&
eb31f147bf4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit b4d87499a5677fbf611eedfa06c1b3d5cdc23914
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14 chmod 600 "\${HOME}/.hg.conf" &&
eb31f147bf4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit b4d87499a5677fbf611eedfa06c1b3d5cdc23914
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15 mafFetch '$genome' '$track' '$bed_file' 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>
eb31f147bf4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit b4d87499a5677fbf611eedfa06c1b3d5cdc23914
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31 </configfiles>
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32 <inputs>
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33 <param name="bed_file" type="data" format="bed" label="Input BED file" help="Input BED file can be either BED6 or BED12"/>
eb31f147bf4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit b4d87499a5677fbf611eedfa06c1b3d5cdc23914
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34 <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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35 <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)"/>
eb31f147bf4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit b4d87499a5677fbf611eedfa06c1b3d5cdc23914
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36 </inputs>
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37 <outputs>
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38 <data name="output" format="maf" from_work_dir="out.maf" label="${tool.name} on ${on_string}:Output MAF"/>
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39 </outputs>
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40 <tests>
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41 <!-- Test 01: Testing with default options -->
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42 <test expect_num_outputs="1">
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43 <param name="bed_file" value="mafFetch.bed"/>
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44 <param name="genome" value="hg19"/>
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45 <param name="track" value="multiz46way"/>
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46 <output name="output" ftype="maf">
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47 <assert_contents>
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48 <has_n_lines n="167"/>
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49 <has_size value="17364"/>
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50 </assert_contents>
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51 </output>
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55
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56 mafFetch is a command-line tool from the UCSC Genome Browser suite that extracts MAF records overlapping regions in a BED file (minimum 3 columns: chrom, start, end) from a specified UCSC database table (e.g., multiz46way for hg19). Outputs alignments to a MAF file using an indexed lookup for efficiency.
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57
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58 ]]></help>
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59 <citations>
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60 <citation type="bibtex">
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61 @misc{mafFetch,
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62 author = {Kent UCSC},
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63 title = {mafFetch: A tool for get overlapping records from an MAF using an index table},
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64 note = {Tool for get overlapping records from an MAF using an index table}
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65 </citation>
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66 </citations>
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67 <creator>
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68 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12" identifier="https://orcid.org/0009-0003-9935-828X"/>
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69 <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
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70 </creator>
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71 </tool>