Mercurial > repos > iuc > trinity

annotate abundance_estimates_to_matrix.xml @ 2:de0af39266ef draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
author iuc
date Mon, 25 Apr 2016 10:02:37 -0400
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de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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1 <tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="2.1.1">
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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2 <description>for a de novo assembly of RNA-Seq data by Trinity</description>
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iuc
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3 <requirements>
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iuc
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4 <requirement type="package" version="2.1.1">trinity</requirement>
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iuc
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5 <requirement type="package" version="1.1.2">bowtie</requirement>
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6 <requirement type="package" version="1.2">samtools</requirement>
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7 <requirement type="package" version="3.12.0">edger</requirement>
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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8 <requirement type="package" version="3.12.0">bioconductor-edger</requirement>
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9 <requirement type="package" version="1.2.28">rsem</requirement>
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10 </requirements>
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11 <stdio>
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12 <exit_code range="1:"/>
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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13 </stdio>
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14 <command><![CDATA[
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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15 #for $entry in $samples:
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16 ln -s "${entry.file}" "${entry.sample_name}.tsv" &&
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17 #end for
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19 abundance_estimates_to_matrix.pl
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21 --est_method ${est_method}
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22 --cross_sample_norm ${additional_params.cross_sample_norm}
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24 #for $entry in $samples:
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25 "${entry.sample_name}.tsv"
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26 #end for
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27 ]]></command>
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28 <inputs>
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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29 <repeat name="samples" title="RSEM abundance estimates for samples">
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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30 <param name="file" label="Add file" type="data" format="tabular"/>
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31 <param name="sample_name" label="Sample name" type="text">
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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32 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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33 </param>
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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34 </repeat>
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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35
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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36 <param type="select" name="est_method" label="Abundance estimation method">
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37 <option value="RSEM">RSEM</option>
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38 <option value="eXpress">eXpress</option>
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39 </param>
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40
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41 <section name="additional_params" title="Additional Options" expanded="False">
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42 <param type="select" name="cross_sample_norm" label="Cross sample normalization">
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43 <option value="TMM">TMM</option>
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44 <option value="UpperQuartile">UpperQuartile</option>
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45 <option value="none">None</option>
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46 </param>
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47 </section>
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48 </inputs>
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49 <outputs>
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50 <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/>
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51 <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/>
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52 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix">
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53 <filter>additional_params['cross_sample_norm'] == "TMM"</filter>
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54 </data>
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55 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix">
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56 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
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57 </data>
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/>
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62 <param name="samples_0|sample_name" value="sample_A"/>
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63 <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/>
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64 <param name="samples_1|sample_name" value="sample_B"/>
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65 <param name="est_method" value="RSEM"/>
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66 <param name="cross_sample_norm" value="TMM"/>
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67 <output name="trans_counts">
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68 <assert_contents>
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69 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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70 <has_n_columns n="3" />
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71 </assert_contents>
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72 </output>
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73 <output name="TPM_no_norm">
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74 <assert_contents>
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75 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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76 <has_n_columns n="3" />
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77 </assert_contents>
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78 </output>
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79 <output name="norm">
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80 <assert_contents>
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81 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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82 <has_n_columns n="3" />
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83 </assert_contents>
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84 </output>
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85 </test>
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86 <test>
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87 <param name="samples_0|file" value="count/rsem_bowtie2/RSEM.genes.results"/>
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88 <param name="samples_0|sample_name" value="sample_A"/>
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89 <param name="samples_1|file" value="count/rsem_bowtie2/RSEM.genes_B.results"/>
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90 <param name="samples_1|sample_name" value="sample_B"/>
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91 <param name="est_method" value="RSEM"/>
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92 <param name="cross_sample_norm" value="TMM"/>
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93 <output name="trans_counts">
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iuc
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94 <assert_contents>
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iuc
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95 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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iuc
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96 <has_n_columns n="3" />
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iuc
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97 </assert_contents>
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98 </output>
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iuc
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99 <output name="TPM_no_norm">
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iuc
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100 <assert_contents>
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iuc
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101 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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iuc
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102 <has_n_columns n="3" />
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iuc
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103 </assert_contents>
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104 </output>
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iuc
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105 <output name="norm">
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iuc
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106 <assert_contents>
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iuc
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107 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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iuc
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108 <has_n_columns n="3" />
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109 </assert_contents>
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110 </output>
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111 </test>
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112 <test>
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113 <param name="samples_0|file" value="count/express_bowtie/results.xprs.genes"/>
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114 <param name="samples_0|sample_name" value="sample_A"/>
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115 <param name="samples_1|file" value="count/express_bowtie/results_B.xprs.genes"/>
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116 <param name="samples_1|sample_name" value="sample_B"/>
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117 <param name="est_method" value="eXpress"/>
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118 <param name="cross_sample_norm" value="TMM"/>
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119 <output name="trans_counts">
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120 <assert_contents>
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121 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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iuc
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122 <has_n_columns n="3" />
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iuc
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123 </assert_contents>
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124 </output>
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iuc
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125 <output name="TPM_no_norm">
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iuc
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126 <assert_contents>
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127 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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iuc
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128 <has_n_columns n="3" />
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129 </assert_contents>
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130 </output>
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131 <output name="norm">
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132 <assert_contents>
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133 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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iuc
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134 <has_n_columns n="3" />
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135 </assert_contents>
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136 </output>
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137 </test>
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138 <test>
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139 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/>
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140 <param name="samples_0|sample_name" value="sample_A"/>
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141 <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/>
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iuc
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142 <param name="samples_1|sample_name" value="sample_B"/>
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143 <param name="est_method" value="RSEM"/>
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144 <param name="cross_sample_norm" value="UpperQuartile"/>
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iuc
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145 <output name="trans_counts">
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iuc
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146 <assert_contents>
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iuc
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147 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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iuc
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148 <has_n_columns n="3" />
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iuc
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149 </assert_contents>
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iuc
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150 </output>
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iuc
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151 <output name="TPM_no_norm">
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iuc
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152 <assert_contents>
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iuc
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153 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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iuc
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154 <has_n_columns n="3" />
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155 </assert_contents>
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156 </output>
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157 <output name="norm" file="count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix" />
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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158 </test>
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159 <test>
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160 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/>
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iuc
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161 <param name="samples_0|sample_name" value="sample_A"/>
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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162 <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/>
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163 <param name="samples_1|sample_name" value="sample_B"/>
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164 <param name="est_method" value="RSEM"/>
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165 <param name="cross_sample_norm" value="none"/>
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166 <output name="trans_counts">
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167 <assert_contents>
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168 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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iuc
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169 <has_n_columns n="3" />
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170 </assert_contents>
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171 </output>
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172 <output name="TPM_no_norm">
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iuc
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173 <assert_contents>
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iuc
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174 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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iuc
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175 <has_n_columns n="3" />
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176 </assert_contents>
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177 </output>
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178 </test>
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179 </tests>
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180 <help>
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181 <![CDATA[
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182 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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183 This tool will combine abundance estimations (produced by 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool) from multiple samples into a single tabular file.
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184 This matrix can then be used by 'RNASeq samples quality check for transcript quantification' and 'Differential Expression Analysis using a Trinity assembly' tools.
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185
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186 **Inputs**
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187
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188 It takes as input multiple results from 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool/
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189 Each sample must have a name, that should be used in subsequent tools.
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190
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191 **Output**
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192
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193 This tool will produce a single matrix file. More details on this page:
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194
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195 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
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196
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197
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198 .. _Trinity: http://trinityrnaseq.github.io
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199 ]]>
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200 </help>
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201
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202 <citations>
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203 <citation type="doi">doi:10.1038/nbt.1883</citation>
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204 </citations>
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205 </tool>
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206