Mercurial > repos > iuc > ucsc_axttomaf

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
author iuc
date Thu, 26 Sep 2024 16:52:23 +0000
parents a030255ee7eb
children
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2
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
iuc
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1 <tool id="ucsc_axtomaf" name="axtToMaf" version="@TOOL_VERSION@+galaxy1" profile="21.05" license="MIT">
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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2 <description>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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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
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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
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6 <token name="@TOOL_VERSION@">469</token>
2
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
iuc
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7 <xml name="sanitize_query">
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
iuc
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8 <sanitizer>
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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9 <valid initial="string.printable">
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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10 <remove value=" "/>
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
iuc
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11 <remove value="&apos;" />
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
iuc
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12 </valid>
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
iuc
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13 <mapping initial="none">
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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14 <add source=" " target=""/>
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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15 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
iuc
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16 </mapping>
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
iuc
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17 </sanitizer>
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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18 </xml>
0
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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19 </macros>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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20 <xrefs>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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21 <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
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22 </xrefs>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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23 <requirements>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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24 <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
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25 </requirements>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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26 <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
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27 <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
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28 axtToMaf
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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29 '$in_axt'
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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30 #if str( $target_reference_index_source.target_reference_index_source_selector ) == "history":
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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31 '${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
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32 #else:
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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33 '$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
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34 #end if
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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35 #if str( $query_reference_index_source.query_reference_index_source_selector ) == "history":
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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36 '${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
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37 #else:
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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38 '$query_reference_index_source.que_ref_index_file.fields.path'
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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39 #end if
2
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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40 #if str($t_prefix)
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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41 -tPrefix='$t_prefix'
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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42 #end if
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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43 #if str($q_prefix)
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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44 -qPrefix='$q_prefix'
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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45 #end if
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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46 $score
021202bf325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
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47 $scoreZero
0
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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48 '$out'
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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49 ]]></command>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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50 <inputs>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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51 <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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52
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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53 <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
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54 <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
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55 <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
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56 <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
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57 </param>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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58 <when 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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59 <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
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60 <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
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61 </param>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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62 </when>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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63 <when 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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64 <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
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65 </when>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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66 </conditional>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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67
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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68 <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
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69 <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
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70 <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
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71 <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
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72 </param>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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73 <when 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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74 <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
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75 <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
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76 </param>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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77 </when>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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78 <when 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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79 <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
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80 </when>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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81 </conditional>
57053821bd4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf commit 329ba037aa5b42a4fcaf0641d588e3600a1ab8dc
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82
2
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83 <param name="t_prefix" type="text" optional="true" label="add this to start of TARGET sequence name in maf" help="Typically organism name and a dot (hg38.) is used">
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84 <expand macro="sanitize_query"/>
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85 </param>
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86 <param name="q_prefix" type="text" optional="true" label="add this to start of QUERY sequence name in maf" help="Typically organism name and a dot (mm10.) is used">
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87 <expand macro="sanitize_query"/>
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88 </param>
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89 <param argument="-score" type="boolean" truevalue="-score" falsevalue="" label="Recalculate score" />
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90 <param argument="-scoreZero" type="boolean" truevalue="-scoreZero" falsevalue="" label="Recalculate score if zero" />
0
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91 </inputs>
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92 <outputs>
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93 <data name="out" format="maf" />
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94 </outputs>
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95 <tests>
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96 <test>
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97 <param name="in_axt" value="1.axt"/>
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98 <conditional name="target_reference_index_source">
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99 <param name="target_reference_index_source_selector" value="history" />
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100 <param name="in_tar_ref_index" value="hg38.fasta.fai"/>
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101 </conditional>
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102 <conditional name="query_reference_index_source">
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103 <param name="query_reference_index_source_selector" value="history" />
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104 <param name="in_que_ref_index" value="mm39.fasta.fai"/>
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105 </conditional>
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106 <output name="out" file="1.maf"/>
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107 </test>
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108 <test>
2
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109 <param name="in_axt" value="2.axt"/>
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110 <conditional name="target_reference_index_source">
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111 <param name="target_reference_index_source_selector" value="history" />
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112 <param name="in_tar_ref_index" value="hg38.noprefix.fasta.fai"/>
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113 </conditional>
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114 <conditional name="query_reference_index_source">
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115 <param name="query_reference_index_source_selector" value="history" />
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116 <param name="in_que_ref_index" value="mm39.noprefix.fasta.fai"/>
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117 </conditional>
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118 <param name="t_prefix" value="hg38." />
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119 <param name="q_prefix" value="mm39." />
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120 <output name="out" file="1.maf"/>
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121 </test>
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122 <test>
0
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123 <param name="in_axt" value="1.axt"/>
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124 <conditional name="target_reference_index_source">
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125 <param name="target_reference_index_source_selector" value="cached" />
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126 <param name="tar_ref_index_file" value="hg38"/>
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127 </conditional>
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128 <conditional name="query_reference_index_source">
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129 <param name="query_reference_index_source_selector" value="cached" />
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130 <param name="que_ref_index_file" value="mm39"/>
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131 </conditional>
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132 <output name="out" file="1.maf"/>
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133 </test>
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134 </tests>
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135 <help><![CDATA[
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136 **What it does**
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137
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138 `axtToMaf`_ is a tool to convert dataset from `axt format`_ to `MAF format`_.
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139
1
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140 For implementation details see axtToMaf's `source code`_.
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141
0
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142 .. _axtToMaf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
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143 .. _axt format: https://genome.ucsc.edu/goldenPath/help/axt.html
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144 .. _MAF format: https://genome.ucsc.edu/FAQ/FAQformat.html#format5
1
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145 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/axtToMaf/axtToMaf.c
0
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146 ]]> </help>
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147 <citations>
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148 <citation type="doi">10.1093/bib/bbs038</citation>
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149 </citations>
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150 </tool>