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annotate reago.xml @ 0:715b263db9f3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
author rnateam
date Tue, 26 Jan 2016 08:17:20 -0500
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children 31a354009216
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0
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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1 <tool id="reago" name="Reago" version="0.1.0">
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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2 <description> to assemble rRNA</description>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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3
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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4 <requirements>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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5 <requirement type="package" version="1.1">infernal</requirement>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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6 <requirement type="package" version="1.5.7">genometools</requirement>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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7 <requirement type="package" version="1.1">reago</requirement>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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8 </requirements>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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9
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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10 <stdio>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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11 <exit_code range="1:" />
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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12 </stdio>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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13
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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14 <command>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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15 <![CDATA[
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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16 #set $r1_output=$os.path.splitext($os.path.basename(str($r1_file)))[0]
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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17 #set $r2_output=$os.path.splitext($os.path.basename(str($r2_file)))[0]
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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18
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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19 python $__tool_directory__/format_reago_input_files.py
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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20 --r1_input "$r1_file"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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21 --r2_input "$r2_file"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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22 --r1_output $r1_output
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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23 --r2_output $r2_output
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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24
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25 &&
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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26 python \${REAGO_DIR}/filter_input.py
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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27 $r1_output
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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28 $r2_output
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29 .
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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30 \${REAGO_DIR}/cm/
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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31 $cm_to_use
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32 "\${GALAXY_SLOTS:-4}"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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33
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34 &&
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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35 python \${REAGO_DIR}/reago.py
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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36 "filtered.fasta"
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37 .
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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38 -l $read_length
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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39 -o $overlap
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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40 -t $tip_size
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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41 -b $path_finding_parameter
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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42 ]]>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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43 </command>
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44
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45 <inputs>
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46 <param name="r1_file" type="data" format="fasta" label="R1 input sequence
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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47 file" help=""/>
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48
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49 <param name="r2_file" type="data" format="fasta" label="R2 input sequence
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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50 file" help=""/>
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51
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52 <param name="read_length" type="integer" min="1" max="1000" value="101"
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53 label="Read length" help="(-l)"/>
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54
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55 <param name="overlap" type="float" min="0" max="1" value="0.8"
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56 label="Overlap" help="(-o)"/>
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57
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58 <param name="tip_size" type="integer" min="0" max="1000" value="30"
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59 label="Tip size" help="(-t)"/>
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60
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61 <param name="path_finding_parameter" type="integer" min="2" max="11"
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62 value="10" label="Path finding parameter" help="(-b)"/>
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63
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64 <param name="cm_to_use" type="select" label="Database to use to to identify 16S reads" help="">
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65 <option value="b">Bacteria only</option>
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66 <option value="a">Archea only</option>
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67 <option value="ab">Bacteria and archea</option>
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68 </param>
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69
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70 </inputs>
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71
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72 <outputs>
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73 <data format="fasta" name="full_genes"
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74 from_work_dir="full_genes.fasta"
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75 label="Full genes of ${on_string} (Framebot)" />
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76 <data format="fasta" name="fragments"
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77 from_work_dir="fragments.fasta"
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78 label="Fragment genes of ${on_string} (Framebot)" />
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79 </outputs>
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80
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81 <tests>
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82 <test>
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83 <param name="r1_file" value="reago_sample_1.fasta"/>
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84 <param name="r2_file" value="reago_sample_2.fasta"/>
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85 <param name="read_length" value="101" />
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86 <param name="overlap" value="0.8" />
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87 <param name="error_correction" value="0.05" />
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88 <param name="tip_size" value="30" />
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89 <param name="path_finding_parameter" value="10"/>
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90 <param name="cm_to_use" value="ab" />
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91 <param name="cpu_nb" value="4" />
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92
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93 <output name="full_genes" file="reago_full_genes.fasta"/>
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94 <output name="fragments" file="reago_fragments.fasta"/>
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95 </test>
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96 </tests>
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97
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98 <help>
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99 <![CDATA[
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100
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101 **What it does**
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102
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103 Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.
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104 More information on `Github repository <https://github.com/chengyuan/reago-1.1>`_.
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105
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106 -----
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107
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108 **Input**
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109
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110 Sequence files with r1 and r2 are required.
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111
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112 -----
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113
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114 **Parameters**
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115
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116 The parameters are
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117
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118 - The overlap percentage
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119 - The threshold for error correction
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120 - The tip size
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121 - The parameter for path finding
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122
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123 -----
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124
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125 **Output**
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126
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127 Reago produces two output files:
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128
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129 - A sequence file with full genes
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130 - A sequence file with fragment genes
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131
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132 ]]>
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133 </help>
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134
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135 <citations>
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136 <citation type="doi">10.1093/bioinformatics/btv231</citation>
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137 </citations>
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138 </tool>