Mercurial > repos > iuc > ucsc_axttomaf

annotate axttomaf.xml @ 1:a030255ee7eb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 303002db06287fb25306020c4391626842f52162
author iuc
date Sun, 22 Sep 2024 07:25:16 +0000
parents 57053821bd4a
children 021202bf325f
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57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
parents:
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1 <tool id="ucsc_axtomaf" name="axtToMaf" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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2 <description>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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3 Convert dataset from axt to MAF format
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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4 </description>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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5 <macros>
1
a030255ee7eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 303002db06287fb25306020c4391626842f52162
iuc
parents: 0
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6 <token name="@TOOL_VERSION@">469</token>
0
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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7 </macros>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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8 <xrefs>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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10 </xrefs>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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11 <requirements>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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12 <requirement type="package" version="@TOOL_VERSION@">ucsc-axttomaf</requirement>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
parents:
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13 </requirements>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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15 <command detect_errors="exit_code"><![CDATA[
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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16 axtToMaf
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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17 '$in_axt'
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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18 #if str( $target_reference_index_source.target_reference_index_source_selector ) == "history":
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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19 '${target_reference_index_source.in_tar_ref_index}'
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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20 #else:
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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21 '$target_reference_index_source.tar_ref_index_file.fields.path'
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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22 #end if
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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23 #if str( $query_reference_index_source.query_reference_index_source_selector ) == "history":
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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24 '${query_reference_index_source.in_que_ref_index}'
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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25 #else:
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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26 '$query_reference_index_source.que_ref_index_file.fields.path'
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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27 #end if
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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28 '$out'
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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29 ]]></command>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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30 <inputs>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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31 <param name="in_axt" format="axt" type="data" label="axt file" />
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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32
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
parents:
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33 <conditional name="target_reference_index_source">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
parents:
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34 <param name="target_reference_index_source_selector" type="select" label="Choose the source for the target reference genome index">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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35 <option value="cached">Built-in</option>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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36 <option value="history">My history</option>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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37 </param>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
parents:
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38 <when value="cached">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
parents:
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39 <param name="tar_ref_index_file" type="select" label="Using reference genome index">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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40 <options from_data_table="fasta_indexes" />
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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41 </param>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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42 </when>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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43 <when value="history">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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44 <param name="in_tar_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for target sequence. Typically a '.fai' file." />
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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45 </when>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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46 </conditional>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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47
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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48 <conditional name="query_reference_index_source">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
parents:
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49 <param name="query_reference_index_source_selector" type="select" label="Choose the source for the target reference genome index">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
parents:
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50 <option value="cached">Built-in</option>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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51 <option value="history">My history</option>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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52 </param>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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53 <when value="cached">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
parents:
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54 <param name="que_ref_index_file" type="select" label="Using reference genome index">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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55 <options from_data_table="fasta_indexes" />
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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56 </param>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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57 </when>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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58 <when value="history">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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59 <param name="in_que_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for query sequence. Typically a '.fai' file." />
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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60 </when>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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61 </conditional>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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62
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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63 </inputs>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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64 <outputs>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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65 <data name="out" format="maf" />
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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66 </outputs>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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67 <tests>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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68 <test>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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69 <param name="in_axt" value="1.axt"/>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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70 <conditional name="target_reference_index_source">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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71 <param name="target_reference_index_source_selector" value="history" />
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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72 <param name="in_tar_ref_index" value="hg38.fasta.fai"/>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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73 </conditional>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
parents:
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74 <conditional name="query_reference_index_source">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
parents:
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75 <param name="query_reference_index_source_selector" value="history" />
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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76 <param name="in_que_ref_index" value="mm39.fasta.fai"/>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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77 </conditional>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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78 <output name="out" file="1.maf"/>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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79 </test>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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80 <test>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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81 <param name="in_axt" value="1.axt"/>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
parents:
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82 <conditional name="target_reference_index_source">
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
iuc
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83 <param name="target_reference_index_source_selector" value="cached" />
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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84 <param name="tar_ref_index_file" value="hg38"/>
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85 </conditional>
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86 <conditional name="query_reference_index_source">
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87 <param name="query_reference_index_source_selector" value="cached" />
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88 <param name="que_ref_index_file" value="mm39"/>
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89 </conditional>
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90 <output name="out" file="1.maf"/>
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94 **What it does**
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95
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96 `axtToMaf`_ is a tool to convert dataset from `axt format`_ to `MAF format`_.
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97
1
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98 For implementation details see axtToMaf's `source code`_.
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99
0
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100 .. _axtToMaf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
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101 .. _axt format: https://genome.ucsc.edu/goldenPath/help/axt.html
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102 .. _MAF format: https://genome.ucsc.edu/FAQ/FAQformat.html#format5
1
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103 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/axtToMaf/axtToMaf.c
0
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104 ]]> </help>
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105 <citations>
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106 <citation type="doi">10.1093/bib/bbs038</citation>
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107 </citations>
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108 </tool>