Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix

annotate abundance_estimates_to_matrix.xml @ 6:74217fbfba4d draft

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author iuc
date Mon, 28 Aug 2017 16:55:13 -0400
parents 8b5039bdf1f6
children 34cefa17a764
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1 <tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.1">
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2 <description>for a de novo assembly of RNA-Seq data by Trinity</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
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8 <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 -->
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9 <requirement type="package" version="0.8.1">salmon</requirement>
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10 <requirement type="package" version="0.43.1">kallisto</requirement>
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11 </expand>
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12 <command detect_errors="aggressive"><![CDATA[
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13 #import re
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14 #for $entry in $samples:
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15 ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' &&
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16 #end for
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18 abundance_estimates_to_matrix.pl
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20 --est_method ${est_method}
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21 --cross_sample_norm ${additional_params.cross_sample_norm}
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23 #for $entry in $samples:
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24 '${re.sub('[^\w\-_]', '_', entry.element_identifier)}'
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25 #end for
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26 ]]></command>
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27 <inputs>
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28 <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" />
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30 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
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31 <option value="RSEM">RSEM</option>
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32 <option value="eXpress">eXpress</option>
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33 <option value="salmon">Salmon</option>
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34 <option value="kallisto">Kallisto</option>
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35 </param>
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36
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37 <section name="additional_params" title="Additional Options" expanded="False">
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38 <param type="select" name="cross_sample_norm" argument="--cross_sample_norm" label="Cross sample normalization">
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39 <option value="TMM">TMM</option>
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40 <option value="UpperQuartile">UpperQuartile</option>
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41 <option value="none">None</option>
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42 </param>
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43 </section>
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44 </inputs>
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45 <outputs>
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46 <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/>
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47 <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/>
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48 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix">
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49 <filter>additional_params['cross_sample_norm'] == "TMM"</filter>
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50 </data>
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51 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix">
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52 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
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53 </data>
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54 </outputs>
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55 <tests>
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56 <test>
1
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57 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
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58 <param name="est_method" value="RSEM"/>
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59 <param name="cross_sample_norm" value="TMM"/>
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60 <output name="trans_counts">
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61 <assert_contents>
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62 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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63 <has_n_columns n="3" />
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64 </assert_contents>
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65 </output>
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66 <output name="TPM_no_norm">
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67 <assert_contents>
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68 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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69 <has_n_columns n="3" />
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70 </assert_contents>
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71 </output>
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72 <output name="norm">
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73 <assert_contents>
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74 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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75 <has_n_columns n="3" />
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76 </assert_contents>
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77 </output>
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78 </test>
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79 <test>
1
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80 <param name="samples" ftype="tabular" value="count/rsem_bowtie2/sample_A,count/rsem_bowtie2/sample_B"/>
0
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81 <param name="est_method" value="RSEM"/>
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82 <param name="cross_sample_norm" value="TMM"/>
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83 <output name="trans_counts">
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84 <assert_contents>
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85 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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86 <has_n_columns n="3" />
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87 </assert_contents>
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diff changeset
88 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
89 <output name="TPM_no_norm">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
90 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
91 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
92 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
93 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
94 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
95 <output name="norm">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
96 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
97 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
98 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
99 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
100 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
101 </test>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
102 <test>
1
fba77b1f69b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents: 0
diff changeset
103 <param name="samples" ftype="tabular" value="count/express_bowtie/sample_A,count/express_bowtie/sample_B"/>
0
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
104 <param name="est_method" value="eXpress"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
105 <param name="cross_sample_norm" value="TMM"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
106 <output name="trans_counts">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
107 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
108 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
109 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
110 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
111 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
112 <output name="TPM_no_norm">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
113 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
114 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
115 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
116 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
117 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
118 <output name="norm">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
119 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
120 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
121 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
122 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
123 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
124 </test>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
125 <test>
1
fba77b1f69b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents: 0
diff changeset
126 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
0
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
127 <param name="est_method" value="RSEM"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
128 <param name="cross_sample_norm" value="UpperQuartile"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
129 <output name="trans_counts">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
130 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
131 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
132 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
133 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
134 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
135 <output name="TPM_no_norm">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
136 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
137 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
138 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
139 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
140 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
141 <output name="norm">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
142 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
143 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
144 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
145 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
146 </test>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
147 <test>
1
fba77b1f69b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents: 0
diff changeset
148 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
0
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
149 <param name="est_method" value="RSEM"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
150 <param name="cross_sample_norm" value="none"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
151 <output name="trans_counts">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
152 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
153 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
154 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
155 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
156 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
157 <output name="TPM_no_norm">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
158 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
159 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
160 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
161 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
162 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
163 </test>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
164 <test>
1
fba77b1f69b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents: 0
diff changeset
165 <param name="samples" ftype="tabular" value="count/salmon/sample_A,count/salmon/sample_B"/>
0
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
166 <param name="est_method" value="salmon"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
167 <param name="cross_sample_norm" value="none"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
168 <output name="trans_counts">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
169 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
170 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
171 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
172 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
173 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
174 <output name="TPM_no_norm">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
175 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
176 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
177 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
178 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
179 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
180 </test>
6
74217fbfba4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
181 <test>
74217fbfba4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
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182 <param name="samples" ftype="tabular" value="count/kallisto/abundance.tsv.genes,count/kallisto/abundance_B.tsv.genes"/>
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183 <param name="est_method" value="kallisto"/>
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184 <param name="cross_sample_norm" value="TMM"/>
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185 <output name="trans_counts">
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186 <assert_contents>
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187 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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188 <has_n_columns n="3" />
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189 </assert_contents>
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190 </output>
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191 <output name="TPM_no_norm">
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192 <assert_contents>
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193 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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194 <has_n_columns n="3" />
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195 </assert_contents>
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196 </output>
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197 <output name="norm">
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198 <assert_contents>
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199 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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200 <has_n_columns n="3" />
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201 </assert_contents>
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202 </output>
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203 </test>
0
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204 </tests>
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205 <help>
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206 <![CDATA[
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207 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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208 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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209 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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210
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211 **Inputs**
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212
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213 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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214 Each sample must have a name, that should be used in subsequent tools.
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215
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216 **Output**
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217
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218 This tool will produce a single matrix file. More details on this page:
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219
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220 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
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221
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222
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223 .. _Trinity: http://trinityrnaseq.github.io
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224 ]]>
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225 </help>
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226
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227 <expand macro="citation" />
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228 </tool>