annotate seal-galaxy-cc1b1911/seal/merge_alignments.xml @ 0:244073d9abc1 draft default tip

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author crs4
date Wed, 15 Oct 2014 09:41:10 -0400
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1
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2 <!--
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3 Copyright (C) 2011-2014 CRS4.
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4
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5 This file is part of Seal.
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6
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7 Seal is free software: you can redistribute it and/or modify it
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8 under the terms of the GNU General Public License as published by the Free
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9 Software Foundation, either version 3 of the License, or (at your option)
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10 any later version.
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11
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12 Seal is distributed in the hope that it will be useful, but
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13 WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
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14 or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
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15 for more details.
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16
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17 You should have received a copy of the GNU General Public License along
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18 with Seal. If not, see <http://www.gnu.org/licenses/>.
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19 -->
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20
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21
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22 <tool id="seal_merge_alignments" name="Merge Alignments" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
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23 <description>Merge a pathset of part-files of alignments into a single well-formatted SAM file</description>
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24 <requirements>
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25 <requirement type="package" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">seal</requirement>
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26 <requirement type="package" version="0.11">pydoop</requirement>
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27 <requirement type="package" version="0.1.3">hadoop-galaxy</requirement>
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28 </requirements>
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29 <command interpreter="python">
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30 #set $ref_path = 'file://' + $reference.fields.path if $reference.fields.path.startswith('/') else $reference.fields.path
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31 merge_alignments.py
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32 $input_data
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33 $output
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34
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35 --annotations ${ref_path}.ann
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36 --sort-order $sort_order
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37
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38 #if $compute_md5:
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39 --md5
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40 #end if
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41
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42 #if $assembly:
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43 --sq-assembly "$assembly"
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44 #end if
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45
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46 #if $rg.set_rg == 'true':
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47 --rg_cn "$rg.rg_cn"
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48 --rg_dt "$rg.rg_dt"
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49 --rg_id "$rg.rg_id"
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50 --rg_lb "$rg.rg_lb"
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51 --rg_pl "$rg.rg_pl"
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52 --rg_pu "$rg.rg_pu"
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53 --rg_sm "$rg.rg_sm"
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54 #end if
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55 </command>
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56
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57 <inputs>
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58 <param name="input_data" type="data" format="pathset" label="Input data" />
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59
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60 <param name="reference" type="select" label="Reference (should be the same one used for alignment)">
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61 <options from_data_table="bwa_0510_indexes" />
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62 </param>
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63
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64 <param name="sort_order" type="select" default="coordinate">
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65 <option value="coordinate">Coordinate</option>
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66 <option value="read_id">Read ID</option>
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67 <option value="unsorted">Unsorted</option>
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68 </param>
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69 <param name="compute_md5" type="boolean" checked="false" label="Whether to compute the MD5 checksums of the reference contigs" />
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70 <param name="assembly" type="text" label="Genome assembly identifier (@SQ AS:XXX tag)" />
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71
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72 <conditional name="rg">
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73 <param name="set_rg" type="boolean" checked="false" label="Set a Read Group line" truevalue="true" falsevalue="false" />
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74
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75 <when value="true">
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76 <param name="rg_cn" type="text" label="Read group center" />
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77 <param name="rg_dt" type="text" label="Read group date" />
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78 <param name="rg_id" type="text" label="Read group id" />
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79 <param name="rg_lb" type="text" label="Read group library" />
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80 <param name="rg_pl" type="text" label="Read group platform" />
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81 <param name="rg_pu" type="text" label="Read group platform unit" />
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82 <param name="rg_sm" type="text" label="Read group sample" />
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83 </when>
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84 </conditional>
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85 </inputs>
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86
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87 <outputs>
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88 <data name="output" format="sam" />
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89 </outputs>
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90
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91 <stdio>
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92 <exit_code range="1:" level="fatal" />
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93 </stdio>
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94
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95 <help>
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96 ReadSort is a Hadoop-based program for sorting reads by alignment position.
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97 For the full help see the `manual &lt;http://biodoop-seal.sourceforge.net/read_sort_index.html&gt;`_.
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98 </help>
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99
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100 </tool>