Mercurial > repos > iuc > ucsc_chainnet

annotate chainnet.xml @ 0:3d8635fc3e51 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
author iuc
date Fri, 30 Aug 2024 17:53:36 +0000
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3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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1 <tool id="ucsc_chainnet" name="chainNet" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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2 <description>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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3 make alignment nets out of alignment chains
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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4 </description>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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5 <macros>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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6 <token name="@TOOL_VERSION@">469</token>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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7 </macros>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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8 <xrefs>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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10 </xrefs>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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11 <requirements>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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12 <requirement type="package" version="@TOOL_VERSION@">ucsc-chainnet</requirement>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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13 </requirements>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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15 <command detect_errors="exit_code"><![CDATA[
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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16 chainNet
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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17 '$in_chain'
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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18 #if str( $target_reference_index_source.target_reference_index_source_selector ) == "history":
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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19 '${target_reference_index_source.in_tar_ref_index}'
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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20 #else:
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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21 '$target_reference_index_source.tar_ref_index_file.fields.path'
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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22 #end if
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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23 #if str( $query_reference_index_source.query_reference_index_source_selector ) == "history":
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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24 '${query_reference_index_source.in_que_ref_index}'
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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25 #else:
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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26 '$query_reference_index_source.que_ref_index_file.fields.path'
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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27 #end if
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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28 '$targetNet'
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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29 '$queryNet'
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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30 #if str($minSpace)
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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31 -minSpace=$minSpace
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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32 #end if
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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33 #if str($minFill)
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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34 -minFill=$minFill
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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35 #end if
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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36 #if str($minScore)
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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37 -minScore=$minScore
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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38 #end if
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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39 $inclHap
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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40 #if str($verbose)
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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41 -verbose=$verbose
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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42 #end if
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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43 ]]></command>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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44 <inputs>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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45 <param name="in_chain" format="chain" type="data" label="Chain dataset" help="Select chain dataset" />
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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46
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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47 <conditional name="target_reference_index_source">
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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48 <param name="target_reference_index_source_selector" type="select" label="Choose the source for the target reference genome index">
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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49 <option value="cached">Built-in</option>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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50 <option value="history">From history</option>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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51 </param>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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52 <when value="cached">
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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53 <param name="tar_ref_index_file" type="select" label="Using reference genome index">
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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54 <options from_data_table="fasta_indexes" />
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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55 </param>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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56 </when>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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57 <when value="history">
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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58 <param name="in_tar_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for target sequence. Typically a '.fai' file." />
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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59 </when>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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60 </conditional>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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61
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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62 <conditional name="query_reference_index_source">
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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63 <param name="query_reference_index_source_selector" type="select" label="Choose the source for the query reference genome index">
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
iuc
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64 <option value="cached">Built-in</option>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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65 <option value="history">From history</option>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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66 </param>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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67 <when value="cached">
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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68 <param name="que_ref_index_file" type="select" label="Using reference genome index">
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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69 <options from_data_table="fasta_indexes" />
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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70 </param>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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71 </when>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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72 <when value="history">
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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73 <param name="in_que_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for query sequence. Typically a '.fai' file." />
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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74 </when>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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75 </conditional>
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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76
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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77 <param argument="-minSpace" type="integer" optional="true" min="0" label="Minimum gap size to fill" help="default 25" />
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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78 <param argument="-minFill" type="integer" optional="true" min="0" label="Minimum fill to record" help="default half of minSpace" />
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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79 <param argument="-minScore" type="integer" optional="true" label="Minimum chain score to consider" help="default 2000" />
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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80 <param argument="-inclHap" type="boolean" optional="true" truevalue="-inclHap" falsevalue="" label="Include query sequences name in the form *_hap*|*_alt*. Normally these are excluded from nets as being haplotype pseudochromosomes." />
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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81 <param argument="-verbose" type="integer" optional="true" label="Verbosity" help="default 1" />
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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82
3d8635fc3e51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
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83 </inputs>
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84 <outputs>
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85 <data name="targetNet" format="ucsc.net" label="${tool.name} on ${on_string}: target.net"/>
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86 <data name="queryNet" format="ucsc.net" label="${tool.name} on ${on_string}: query.net" />
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87 </outputs>
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88 <tests>
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89 <test expect_num_outputs="2">
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90 <param name="in_chain" value="input.chain" />
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91 <conditional name="target_reference_index_source">
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92 <param name="target_reference_index_source_selector" value="history" />
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93 <param name="in_tar_ref_index" value="hg38.chr20.chunk.fasta.fai"/>
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94 </conditional>
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95 <conditional name="query_reference_index_source">
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96 <param name="query_reference_index_source_selector" value="history" />
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97 <param name="in_que_ref_index" value="mm39.chr2.chunk.fasta.fai"/>
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98 </conditional>
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99 <output name="targetNet" file="target.net"/>
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100 <output name="queryNet" file="query.net"/>
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101 </test>
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102 <test expect_num_outputs="2">
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103 <param name="in_chain" value="input.chain" />
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104 <conditional name="target_reference_index_source">
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105 <param name="target_reference_index_source_selector" value="cached" />
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106 <param name="tar_ref_index_file" value="hg38.chr20.chunk"/>
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107 </conditional>
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108 <conditional name="query_reference_index_source">
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109 <param name="query_reference_index_source_selector" value="cached" />
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110 <param name="que_ref_index_file" value="mm39.chr2.chunk"/>
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111 </conditional>
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112 <output name="targetNet" file="target.net"/>
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113 <output name="queryNet" file="query.net"/>
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114 </test>
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115 <test expect_num_outputs="2">
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116 <param name="in_chain" value="input.chain" />
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117 <param name="minScore" value="1200" />
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118 <conditional name="target_reference_index_source">
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119 <param name="target_reference_index_source_selector" value="cached" />
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120 <param name="tar_ref_index_file" value="hg38.chr20.chunk"/>
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121 </conditional>
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122 <conditional name="query_reference_index_source">
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123 <param name="query_reference_index_source_selector" value="history" />
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124 <param name="in_que_ref_index" value="mm39.chr2.chunk.fasta.fai"/>
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125 </conditional>
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126 <output name="targetNet" file="target.1200.net"/>
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127 <output name="queryNet" file="query.1200.net"/>
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128 </test>
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129 </tests>
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130 <help><![CDATA[
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131 **What it does**
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132
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133 `chainNet`_ is a tool that makes alignment nets out of `alignment chains`_.
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134 It outputs two files in the `ucsc.net`_ format -- one for the target sequence and one for the query sequence.
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135
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136 For implementation details see ChainNet's `source code`_.
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137
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138 .. _chainNet: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
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139 .. _ucsc.net: https://genome.ucsc.edu/goldenPath/help/net.html
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140 .. _alignment chains: https://genome.ucsc.edu/goldenPath/help/chain.html
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141 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/chainNet/chainNet.c
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142 ]]> </help>
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143 <citations>
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144 <citation type="doi">10.1093/bib/bbs038</citation>
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145 </citations>
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146 </tool>