Mercurial > repos > iuc > semibin

annotate semibin.xml @ 2:9de6b5e570df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
author iuc
date Tue, 25 Mar 2025 15:52:22 +0000
parents 2eeff5d4a5de
children 8673617e7e09
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d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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1 <tool id="semibin" name="SemiBin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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2 <description>
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3 for Semi-supervised Metagenomic Binning
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="biotools"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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9 <expand macro="requirements"/>
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10 <expand macro="version"/>
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11 <command detect_errors="exit_code"><![CDATA[
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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12 #import re
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13 @BAM_FILES@
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14 @FASTA_FILES@
2
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15 SemiBin2
0
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16 #if $mode.select == 'single' or $mode.select == 'co'
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17 single_easy_bin
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18 #if $mode.select == 'single' and str($mode.environment) != ''
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19 --environment '$mode.environment'
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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20 #end if
2
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21 #if $mode.ref.select == "cached":
0
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22 --reference-db-data-dir '$mode.ref.cached_db.fields.path'
2
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23 #end if
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24 #if $mode.ref.select == "taxonomy"
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25 --taxonomy-annotation-table '$mode.ref.taxonomy_annotation_table'
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26 #end if
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27 #else
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28 multi_easy_bin
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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29 --separator '$separator'
2
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30 #if $mode.ref.select == "cached":
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d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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31 --reference-db-data-dir '$mode.ref.cached_db.fields.path'
2
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32 #end if
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33 #if $mode.ref.select == "taxonomy"
0
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34 --taxonomy-annotation-table
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35 #for $e in $mode.ref.taxonomy_annotation_table
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36 '$e'
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37 #end for
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38 #end if
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39 #end if
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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40 --input-fasta 'contigs.fasta'
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41 --input-bam *.bam
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42 --output 'output'
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43 --cannot-name 'cannot'
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44 @MIN_LEN@
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45 --orf-finder '$orf_finder'
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46 --random-seed $random_seed
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47
2
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48 #if $annot.ml_threshold:
0
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49 --ml-threshold $annot.ml_threshold
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50 #end if
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51 --epoches $training.epoches
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52 --batch-size $training.batch_size
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53 --max-node $bin.max_node
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54 --max-edges $bin.max_edges
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55 --minfasta-kbs $bin.minfasta_kbs
2
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56 #if ($mode.select == 'single' or $mode.select == 'co') and $extra_output and "pre_reclustering_bins" in $extra_output
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57 --write-pre-reclustering-bins
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58 #end if
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59 --compression none
0
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60 --threads \${GALAXY_SLOTS:-1}
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61 --processes \${GALAXY_SLOTS:-1}
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62 &&
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63 echo "output" &&
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64 ls output
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65 ]]></command>
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66 <inputs>
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67 <conditional name="mode">
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68 <expand macro="mode_select"/>
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69 <when value="single">
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70 <expand macro="input-fasta-single"/>
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71 <expand macro="input-bam-single"/>
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72 <expand macro="ref-single"/>
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73 <expand macro="environment"/>
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74 </when>
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75 <when value="co">
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76 <expand macro="input-fasta-single"/>
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77 <expand macro="input-bam-multi"/>
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78 <expand macro="ref-single"/>
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79 </when>
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80 <when value="multi">
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81 <expand macro="input-fasta-multi"/>
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82 <expand macro="input-bam-multi"/>
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83 <expand macro="ref-multi"/>
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84 </when>
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85 </conditional>
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86 <expand macro="min_len"/>
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87 <expand macro="orf-finder"/>
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88 <expand macro="random-seed"/>
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89 <section name="annot" title="Contig annotations" expanded="true">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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90 <expand macro="ml-threshold"/>
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91 </section>
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92 <section name="training" title="Training">
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93 <expand macro="epoches"/>
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94 <expand macro="batch-size"/>
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95 </section>
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96 <section name="bin" title="Binning">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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97 <expand macro="max-node"/>
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98 <expand macro="max-edges"/>
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99 <expand macro="minfasta-kbs"/>
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100 </section>
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101 <param name="extra_output" type="select" multiple="true" optional="true" label="Extra outputs" help="In addition to the training data">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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102 <option value="data">Training data</option>
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103 <option value="coverage">Coverage files</option>
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104 <option value="contigs">Contigs (if multiple sample)</option>
2
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105 <option value="pre_reclustering_bins">Pre-reclustering bins (only single sample and co-assembly)</option>
0
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106 </param>
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107 </inputs>
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108 <outputs>
2
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109 <collection name="output_pre_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">
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110 <filter>mode["select"]!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>
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111 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_prerecluster_bins"/>
0
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112 </collection>
2
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113 <collection name="output_after_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering">
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114 <filter>mode["select"]!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>
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115 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_recluster_bins"/>
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116 </collection>
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117 <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins">
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118 <filter>mode["select"]!="multi" and not "pre_reclustering_bins" in extra_output</filter>
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119 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins"/>
0
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120 </collection>
1
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121 <collection name="multi_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering (multi_bins)">
0
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122 <filter>mode["select"]=="multi"</filter>
2
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123 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/bins"/>
0
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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124 </collection>
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125 <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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126 <filter>(mode["select"]=="single" or mode["select"]=="co") and extra_output and "data" in extra_output</filter>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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127 </data>
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128 <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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129 <filter>(mode["select"]=="single" or mode["select"]=="co") and extra_output and "data" in extra_output</filter>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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130 </data>
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131 <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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132 <filter>mode["select"]=="multi" and extra_output and "data" in extra_output</filter>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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133 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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134 </collection>
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diff changeset
135 <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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diff changeset
136 <filter>mode["select"]=="multi" and extra_output and "data" in extra_output</filter>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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137 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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138 </collection>
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139 <expand macro="generate_sequence_features_extra_outputs"/>
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140 </outputs>
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141 <tests>
2
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142 <test expect_num_outputs="5">
0
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143 <conditional name="mode">
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144 <param name="select" value="single"/>
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145 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
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146 <param name="input_bam" ftype="bam" value="input_single.bam"/>
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147 <conditional name="ref">
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148 <param name="select" value="taxonomy"/>
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149 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
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150 </conditional>
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151 <param name="environment" value="human_gut"/>
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152 </conditional>
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153 <conditional name="min_len">
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154 <param name="method" value="min-len"/>
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155 <param name="min_len" value="0" />
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156 </conditional>
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157 <param name="orf_finder" value="prodigal"/>
2
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158 <param name="random_seed" value="0"/>
0
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159 <section name="training">
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160 <param name="epoches" value="20"/>
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161 <param name="batch_size" value="2048"/>
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162 </section>
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163 <section name="bin">
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164 <param name="max_node" value="1"/>
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165 <param name="max_edges" value="200"/>
2
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166 <param name="minfasta_kbs" value="200"/>
0
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167 </section>
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168 <param name="extra_output" value="data,coverage,contigs"/>
2
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169 <output_collection name="output_bins" count="0"/>
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170 <output name="single_data" ftype="csv">
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171 <assert_contents>
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172 <has_text text="g1k_0"/>
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173 <has_text text="g4k_7"/>
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174 </assert_contents>
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175 </output>
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176 <output name="single_data_split" ftype="csv">
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177 <assert_contents>
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178 <has_text text="g1k_0_1"/>
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179 <has_text text="g1k_6_2"/>
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180 </assert_contents>
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181 </output>
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182 <output name="single_cov" ftype="csv">
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183 <assert_contents>
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184 <has_text text="g1k_0"/>
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185 <has_text text="0.027"/>
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186 </assert_contents>
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187 </output>
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188 <output name="single_split_cov" ftype="csv">
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189 <assert_contents>
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190 <has_size value="1" delta="1"/>
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191 </assert_contents>
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192 </output>
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193 </test>
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194 <test expect_num_outputs="5">
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195 <conditional name="mode">
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196 <param name="select" value="single"/>
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197 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
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198 <param name="input_bam" ftype="bam" value="input_single.bam"/>
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199 <conditional name="ref">
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200 <param name="select" value="ml"/>
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201 </conditional>
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202 <param name="environment" value="human_gut"/>
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203 </conditional>
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204 <conditional name="min_len">
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205 <param name="method" value="min-len"/>
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206 <param name="min_len" value="0" />
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207 </conditional>
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208 <param name="orf_finder" value="prodigal"/>
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209 <param name="random_seed" value="0"/>
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210 <section name="training">
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211 <param name="epoches" value="20"/>
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212 <param name="batch_size" value="2048"/>
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213 </section>
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214 <section name="bin">
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215 <param name="max_node" value="1"/>
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216 <param name="max_edges" value="200"/>
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217 <param name="minfasta_kbs" value="200"/>
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218 </section>
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219 <param name="extra_output" value="data,coverage,contigs"/>
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220 <output_collection name="output_bins" count="0"/>
0
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221 <output name="single_data" ftype="csv">
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222 <assert_contents>
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223 <has_text text="g1k_0"/>
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224 <has_text text="g4k_7"/>
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225 </assert_contents>
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226 </output>
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227 <output name="single_data_split" ftype="csv">
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228 <assert_contents>
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229 <has_text text="g1k_0_1"/>
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230 <has_text text="g1k_6_2"/>
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231 </assert_contents>
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232 </output>
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233 <output name="single_cov" ftype="csv">
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234 <assert_contents>
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235 <has_text text="g1k_0"/>
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236 <has_text text="0.027"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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237 </assert_contents>
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238 </output>
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239 <output name="single_split_cov" ftype="csv">
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240 <assert_contents>
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241 <has_size value="1" delta="1"/>
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242 </assert_contents>
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243 </output>
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244 </test>
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245 <test expect_num_outputs="3">
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246 <conditional name="mode">
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247 <param name="select" value="co"/>
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248 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
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249 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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250 <conditional name="ref">
2
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parents: 1
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251 <param name="select" value="ml"/>
0
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252 </conditional>
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253 </conditional>
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254 <conditional name="min_len">
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255 <param name="method" value="ratio"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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256 <param name="ratio" value="0.05"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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257 </conditional>
2
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258 <param name="orf_finder" value="fast-naive"/>
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259 <param name="random_seed" value="0"/>
0
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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260 <section name="training">
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261 <param name="epoches" value="20"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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262 <param name="batch_size" value="2048"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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263 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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264 <section name="bin">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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265 <param name="max_node" value="1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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266 <param name="max_edges" value="200"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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267 <param name="minfasta_kbs" value="200"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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268 </section>
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269 <param name="extra_output" value="coverage"/>
2
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270 <output_collection name="output_bins" count="0"/>
0
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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271 <output_collection name="co_cov" count="5">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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272 <element name="0" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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273 <assert_contents>
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274 <has_text text="g1k_0"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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275 <has_text text="g2k_7"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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276 </assert_contents>
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277 </element>
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278 <element name="1" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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279 <assert_contents>
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iuc
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280 <has_text text="g1k_0"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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281 <has_text text="g2k_7"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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282 </assert_contents>
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283 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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284 <element name="4" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
285 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
286 <has_text text="g1k_0"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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287 <has_text text="g2k_7"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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288 </assert_contents>
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289 </element>
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iuc
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290 </output_collection>
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iuc
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291 <output_collection name="co_split_cov" count="5">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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292 <element name="0" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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293 <assert_contents>
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iuc
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294 <has_text text="g1k_0_1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
295 <has_text text="g2k_7_2"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
296 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
297 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
298 <element name="1" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
299 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
300 <has_text text="g1k_0_1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
301 <has_text text="g2k_7_2"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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302 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
303 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
304 <element name="2" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
305 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
306 <has_text text="g1k_0_1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
307 <has_text text="g2k_7_2"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
308 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
309 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
310 </output_collection>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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diff changeset
311 </test>
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
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diff changeset
312 <test expect_num_outputs="3">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
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diff changeset
313 <conditional name="mode">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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diff changeset
314 <param name="select" value="co"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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diff changeset
315 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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diff changeset
316 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
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diff changeset
317 <conditional name="ref">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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318 <param name="select" value="taxonomy"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
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319 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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320 </conditional>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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321 </conditional>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
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diff changeset
322 <conditional name="min_len">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
323 <param name="method" value="ratio"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
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diff changeset
324 <param name="ratio" value="0.05"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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325 </conditional>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
326 <param name="orf_finder" value="fast-naive"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
327 <param name="random_seed" value="0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
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diff changeset
328 <section name="training">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
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diff changeset
329 <param name="epoches" value="20"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
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330 <param name="batch_size" value="2048"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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331 </section>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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diff changeset
332 <section name="bin">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
333 <param name="max_node" value="1"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
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diff changeset
334 <param name="max_edges" value="200"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
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335 <param name="minfasta_kbs" value="200"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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336 </section>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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diff changeset
337 <param name="extra_output" value="coverage"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
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diff changeset
338 <output_collection name="output_bins" count="0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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diff changeset
339 <output_collection name="co_cov" count="5">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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340 <element name="0" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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341 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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342 <has_text text="g1k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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343 <has_text text="g2k_7"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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344 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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345 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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346 <element name="1" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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347 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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348 <has_text text="g1k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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349 <has_text text="g2k_7"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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350 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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351 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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352 <element name="4" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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353 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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354 <has_text text="g1k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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355 <has_text text="g2k_7"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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356 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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357 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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358 </output_collection>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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359 <output_collection name="co_split_cov" count="5">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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360 <element name="0" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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361 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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362 <has_text text="g1k_0_1"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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363 <has_text text="g2k_7_2"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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364 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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365 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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366 <element name="1" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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367 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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368 <has_text text="g1k_0_1"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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369 <has_text text="g2k_7_2"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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370 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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371 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
372 <element name="2" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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373 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
374 <has_text text="g1k_0_1"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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375 <has_text text="g2k_7_2"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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376 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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377 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
378 </output_collection>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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379 </test>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
380 <test expect_num_outputs="3">
1
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
381 <conditional name="mode">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
382 <param name="select" value="co"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
383 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
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384 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
385 <conditional name="ref">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
386 <param name="select" value="taxonomy"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
387 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
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388 </conditional>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
389 </conditional>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
390 <conditional name="min_len">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
391 <param name="method" value="ratio"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
392 <param name="ratio" value="0.05"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
393 </conditional>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
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394 <param name="orf_finder" value="fraggenescan"/>
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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395 <param name="random_seed" value="0"/>
1
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
396 <section name="training">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
397 <param name="epoches" value="20"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
398 <param name="batch_size" value="2048"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
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diff changeset
399 </section>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
400 <section name="bin">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
401 <param name="max_node" value="1"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
402 <param name="max_edges" value="200"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
403 <param name="minfasta_kbs" value="200"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
404 </section>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
405 <param name="extra_output" value="coverage"/>
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
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406 <output_collection name="output_bins" count="0"/>
1
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
407 <output_collection name="co_cov" count="5">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
408 <element name="0" ftype="csv">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
409 <assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
410 <has_text text="g1k_0"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
411 <has_text text="g2k_7"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
412 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
413 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
414 <element name="1" ftype="csv">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
415 <assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
416 <has_text text="g1k_0"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
417 <has_text text="g2k_7"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
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418 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
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419 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
420 <element name="4" ftype="csv">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
421 <assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
422 <has_text text="g1k_0"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
423 <has_text text="g2k_7"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
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424 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
425 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
426 </output_collection>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
427 <output_collection name="co_split_cov" count="5">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
428 <element name="0" ftype="csv">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
429 <assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
430 <has_text text="g1k_0_1"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
431 <has_text text="g2k_7_2"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
432 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
433 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
434 <element name="1" ftype="csv">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
435 <assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
436 <has_text text="g1k_0_1"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
437 <has_text text="g2k_7_2"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
438 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
439 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
440 <element name="2" ftype="csv">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
441 <assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
442 <has_text text="g1k_0_1"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
443 <has_text text="g2k_7_2"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
444 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
445 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
446 </output_collection>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
447 </test>
0
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
448 <test expect_num_outputs="1">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
449 <conditional name="mode">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
450 <param name="select" value="single"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
451 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
452 <param name="input_bam" ftype="bam" value="input_single.bam"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
453 <conditional name="ref">
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
454 <param name="select" value="cached"/>
0
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
455 <param name="cached_db" value="test-db"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
456 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
457 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
458 <conditional name="min_len">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
459 <param name="method" value="ratio"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
460 <param name="ratio" value="0.05"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
461 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
462 <param name="orf_finder" value="fraggenescan"/>
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
463 <param name="random_seed" value="0"/>
0
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
464 <section name="training">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
465 <param name="epoches" value="20"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
466 <param name="batch_size" value="2048"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
467 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
468 <section name="bin">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
469 <param name="max_node" value="1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
470 <param name="max_edges" value="200"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
471 <param name="minfasta_kbs" value="200"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
472 </section>
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
473 <output_collection name="output_bins" count="1">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
474 <element name="SemiBin_30" ftype="fasta">
0
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
475 <assert_contents>
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
476 <has_text text=">g3k_0"/>
0
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
477 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
478 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
479 </output_collection>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
480 </test>
1
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
481 <test expect_num_outputs="2">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
482 <conditional name="mode">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
483 <param name="select" value="single"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
484 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
485 <param name="input_bam" ftype="bam" value="input_single.bam"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
486 <conditional name="ref">
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
487 <param name="select" value="cached"/>
1
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
488 <param name="cached_db" value="test-db"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
489 </conditional>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
490 </conditional>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
491 <conditional name="min_len">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
492 <param name="method" value="ratio"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
493 <param name="ratio" value="0.05"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
494 </conditional>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
495 <param name="orf_finder" value="fraggenescan"/>
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
496 <param name="random_seed" value="0"/>
1
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
497 <section name="training">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
498 <param name="epoches" value="20"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
499 <param name="batch_size" value="2048"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
500 </section>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
501 <section name="bin">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
502 <param name="max_node" value="1"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
503 <param name="max_edges" value="200"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
504 <param name="minfasta_kbs" value="200"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
505 </section>
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
506 <param name="extra_output" value="pre_reclustering_bins"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
507 <output_collection name="output_pre_recluster_bins" count="3">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
508 <element name="SemiBin_0" ftype="fasta">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
509 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
510 <has_text text="g1k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
511 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
512 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
513 <element name="SemiBin_1" ftype="fasta">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
514 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
515 <has_text text="g2k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
516 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
517 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
518 <element name="SemiBin_2" ftype="fasta">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
519 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
520 <has_text text="g3k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
521 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
522 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
523 </output_collection>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
524 <output_collection name="output_after_recluster_bins" count="1">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
525 <element name="SemiBin_30" ftype="fasta">
1
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
526 <assert_contents>
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
527 <has_text text="g3k_0"/>
1
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
528 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
529 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
530 </output_collection>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
531 </test>
0
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
532 <test expect_num_outputs="8">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
533 <conditional name="mode">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
534 <param name="select" value="multi"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
535 <conditional name="multi_fasta">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
536 <param name="select" value="concatenated"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
537 <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
538 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
539 <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
540 <conditional name="ref">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
541 <param name="select" value="taxonomy"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
542 <param name="taxonomy_annotation_table" value="taxonomy.tsv,taxonomy_2.tsv,taxonomy_3.tsv,taxonomy_4.tsv,taxonomy_5.tsv,taxonomy_6.tsv,taxonomy_7.tsv,taxonomy_8.tsv,taxonomy_9.tsv,taxonomy_10.tsv"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
543 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
544 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
545 <conditional name="min_len">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
546 <param name="method" value="ratio"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
547 <param name="ratio" value="0.05"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
548 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
549 <param name="orf_finder" value="fraggenescan"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
550 <param name="random_seed" value="0"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
551 <section name="training">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
552 <param name="epoches" value="20"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
553 <param name="batch_size" value="2048"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
554 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
555 <section name="bin">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
556 <param name="max_node" value="1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
557 <param name="max_edges" value="200"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
558 <param name="minfasta_kbs" value="200"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
559 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
560 <param name="extra_output" value="data,coverage,contigs"/>
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
561 <output_collection name="multi_bins" count="0"/>
0
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
562 <output_collection name="multi_data" count="10">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
563 <element name="S8" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
564 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
565 <has_text text="g1k_0,"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
566 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
567 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
568 </output_collection>
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
569 <output_collection name="multi_data_split" count="10">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
570 <element name="S8" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
571 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
572 <has_text text="g1k_0_1,"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
573 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
574 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 1
diff changeset
575 </output_collection>
0
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
576 <output_collection name="multi_cov" count="10">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
577 <element name="8" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
578 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
579 <has_text text="S1:g1k_5,"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
580 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
581 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
582 </output_collection>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
583 <output_collection name="multi_cov_sample" count="10">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
584 <element name="S8" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
585 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
586 <has_text text="g1k_3"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
587 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
588 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
589 </output_collection>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
590 <output_collection name="multi_split_cov" count="10">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
591 <element name="8" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
592 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
593 <has_text text="S1:g1k_5_1,0."/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
594 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
595 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
596 </output_collection>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
597 <output_collection name="multi_split_cov_sample" count="10">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
598 <element name="S8" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
parents:
diff changeset
599 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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600 <has_text text="g1k_3_1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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601 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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602 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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603 </output_collection>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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604 <output_collection name="multi_contigs" count="10">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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605 <element name="S8" ftype="fasta">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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606 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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607 <has_text text=">g1k_0"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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608 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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609 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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610 </output_collection>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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611 </test>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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612 </tests>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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613 <help><![CDATA[
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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614 @HELP_HEADER@
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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615
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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616 Inputs
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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617 ======
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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618
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
iuc
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619 @HELP_INPUT_FASTA@
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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620 @HELP_INPUT_BAM@
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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621
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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622 ]]></help>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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623 <expand macro="citations"/>
2
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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624 </tool>