Mercurial > repos > devteam > picard
annotate picard_ReorderSam.xml @ 26:fc3866ddc7b6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
author | iuc |
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date | Mon, 22 Aug 2022 09:54:37 +0000 |
parents | e65f2d5fd3d8 |
children | c943f4a04af0 |
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486d7500da69
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
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1 <tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
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4740a2548206
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <description>reorder reads to match ordering in reference sequences</description> |
4740a2548206
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <macros> |
4740a2548206
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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4 <import>picard_macros.xml</import> |
4740a2548206
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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5 <token name="@WRAPPER_VERSION@">1</token> |
4740a2548206
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 </macros> |
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e65f2d5fd3d8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
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7 <xrefs> |
e65f2d5fd3d8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
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8 <xref type="bio.tools">picard_reordersam</xref> |
e65f2d5fd3d8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
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9 </xrefs> |
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4740a2548206
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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10 <expand macro="requirements" /> |
4740a2548206
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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11 <command detect_errors="exit_code"><![CDATA[ |
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52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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12 @java_options@ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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13 @symlink_element_identifier@ |
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52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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14 #set $picard_dict = "localref.dict" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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15 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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16 |
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08f69add4d06
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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17 ln -s "${reference_source.ref_file}" "${ref_fasta}" && |
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e417b1d6288d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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18 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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19 #if str( $reference_source.reference_source_selector ) == "history": |
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e417b1d6288d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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20 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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21 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" |
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52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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22 QUIET=true |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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23 VERBOSITY=ERROR |
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a5a13ea16d17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
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24 @TMPDIR_OPTION@ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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25 |
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08f69add4d06
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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26 && |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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27 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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28 #else: |
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e417b1d6288d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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29 |
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52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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30 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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31 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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32 #end if |
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e417b1d6288d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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33 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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34 picard |
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35 ReorderSam |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
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36 INPUT='$escaped_element_identifier' |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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37 OUTPUT="${outFile}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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38 REFERENCE="${ref_fasta}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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39 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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40 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}" |
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e417b1d6288d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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41 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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42 VALIDATION_STRINGENCY="${validation_stringency}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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43 QUIET=true |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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44 VERBOSITY=ERROR |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
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45 @TMPDIR_OPTION@ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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46 |
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47 ]]></command> |
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48 |
0 | 49 <inputs> |
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50 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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51 <conditional name="reference_source"> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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52 <param name="reference_source_selector" type="select" label="Load reference genome from"> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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53 <option value="cached">Local cache</option> |
0 | 54 <option value="history">History</option> |
55 </param> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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56 <when value="cached"> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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57 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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58 <options from_data_table="picard_indexes"> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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59 <filter type="sort_by" column="2" /> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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60 <validator type="no_options" message="No indexes are available" /> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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61 </options> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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62 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> |
0 | 63 </param> |
64 </when> | |
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65 <when value="history"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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66 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" /> |
0 | 67 </when> |
68 </conditional> | |
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69 |
52fdfc45590a
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70 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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71 <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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72 <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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73 <expand macro="VS" /> |
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74 |
0 | 75 </inputs> |
76 <outputs> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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77 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/> |
0 | 78 </outputs> |
79 <tests> | |
80 <test> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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81 <param name="reference_source_selector" value="history" /> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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82 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" /> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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83 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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84 <param name="allow_incomplete_dict_concordance" value="false"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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85 <param name="allow_contig_length_discordance" value="false"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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86 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/> |
0 | 87 </test> |
88 </tests> | |
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89 |
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90 |
0 | 91 <help> |
92 | |
93 .. class:: infomark | |
94 | |
95 **Purpose** | |
96 | |
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97 ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped. |
0 | 98 |
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99 @dataset_collections@ |
0 | 100 |
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101 ---- |
0 | 102 |
103 .. class:: warningmark | |
104 | |
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105 Not to be confused with **SortSam**. |
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106 |
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107 @description@ |
0 | 108 |
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109 ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean |
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110 S=Boolean If true, then allows only a partial overlap of the BAM contigs with the new reference |
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111 sequence contigs. By default, this tool requires a corresponding contig in the new |
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112 reference for each read contig Default value: false. Possible values: {true, false} |
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113 |
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114 ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean |
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115 U=Boolean If true, then permits mapping from a read contig to a new reference contig with the same |
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116 name but a different length. Highly dangerous, only use if you know what you are doing. |
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117 Default value: false. Possible values: {true, false} |
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119 @more_info@ |
0 | 120 </help> |
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121 <expand macro="citations" /> |
0 | 122 </tool> |