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annotate reago.xml @ 0:04749f9173e5 draft default tip

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
author bebatut
date Tue, 08 Dec 2015 10:35:06 -0500
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0
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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1 <tool id="reago" name="Reago" version="0.1.0">
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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2 <description> to assemble rRNA</description>
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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3
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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4 <requirements>
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5 <requirement type="package" version="1.1">infernal</requirement>
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6 <requirement type="package" version="1.5.7">genometools</requirement>
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7 <requirement type="package" version="1.1">reago</requirement>
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8 </requirements>
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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10 <stdio>
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11 <exit_code range="1:" />
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12 </stdio>
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04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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14 <command>
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15 <![CDATA[
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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16 #set $r1_output=$os.path.splitext($os.path.basename(str($r1_file)))[0]
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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17 #set $r2_output=$os.path.splitext($os.path.basename(str($r2_file)))[0]
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18
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19 python $__tool_directory__/format_reago_input_files.py
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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20 --r1_input $r1_file
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21 --r2_input $r2_file
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22 --r1_output $r1_output
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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23 --r2_output $r2_output
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24
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25 ;
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26 python \${REAGO_DIR}/filter_input.py
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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27 $r1_output
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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28 $r2_output
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29 .
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30 \${REAGO_DIR}/cm/ ab 4
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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31
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32 ;
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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33 python \${REAGO_DIR}/reago.py
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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34 filtered.fasta
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35 .
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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36 -l $read_length
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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37 -o $overlap
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38 -t $tip_size
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39 -b $path_finding_parameter
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40 ]]>
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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41 </command>
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42
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43 <inputs>
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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44 <param name="r1_file" type="data" format="fasta" label="R1 input sequence
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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45 file" help=""/>
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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46 <param name="r2_file" type="data" format="fasta" label="R2 input sequence
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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47 file" help=""/>
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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48 <param name="read_length" type="integer" min="1" max="1000" value="101"
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49 label="Read length" help=""/>
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50 <param name="overlap" type="float" min="0" max="1" value="0.8"
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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51 label="Overlap" help=""/>
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52 <param name="tip_size" type="integer" min="0" max="1000" value="30"
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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53 label="Tip size" help=""/>
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54 <param name="path_finding_parameter" type="integer" min="2" max="11"
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55 value="10" label="Path finding parameter" help=""/>
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56 </inputs>
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57
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58 <outputs>
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59 <data format="fasta" name="full_genes"
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60 from_work_dir="full_genes.fasta"
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61 label="Full genes of ${on_string} (Framebot)" />
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62 <data format="fasta" name="fragments"
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63 from_work_dir="fragments.fasta"
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64 label="Fragment genes of ${on_string} (Framebot)" />
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65 </outputs>
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66
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67 <tests>
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68 <test>
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69 <param name="r1_file" value="reago_sample_1.fasta"/>
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70 <param name="r2_file" value="reago_sample_2.fasta"/>
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71 <param name="read_length" value="101" />
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72 <param name="overlap" value="0.8" />
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73 <param name="error_correction" value="0.05" />
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74 <param name="tip_size" value="30" />
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75 <param name="path_finding_parameter" value="10"/>
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76
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77 <output name="full_genes" file="reago_full_genes.fasta"/>
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78 <output name="fragments" file="reago_fragments.fasta"/>
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79 </test>
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80 </tests>
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81
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82 <help>
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83 <![CDATA[
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84
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85 **What it does**
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86
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87 Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.
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88 More information on `Github repository <https://github.com/chengyuan/reago-1.1>`_.
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89
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90 -----
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91
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92 **Input**
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93
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94 Sequence files with r1 and r2 are required.
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95
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96 -----
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97
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98 **Parameters**
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99
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100 The parameters are
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101
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102 - The overlap percentage
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103 - The threshold for error correction
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104 - The tip size
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105 - The parameter for path finding
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106
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107 -----
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108
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109 **Output**
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110
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111 Reago produces two output files:
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112
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113 - A sequence file with full genes
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114 - A sequence file with fragment genes
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115
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116 ]]>
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117 </help>
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118
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119 <citations>
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120 <citation type="doi">10.1093/bioinformatics/btv231</citation>
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121 </citations>
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122 </tool>