Mercurial > repos > lgueguen > sartools
comparison pre_sartools.xml @ 4:05c9b1a7f44e draft default tip
Uploaded new release 1.7.3
| author | lgueguen |
|---|---|
| date | Thu, 07 Jan 2021 11:12:01 +0000 |
| parents | de6d0b7c17af |
| children |
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| 3:de6d0b7c17af | 4:05c9b1a7f44e |
|---|---|
| 1 <tool id="presartools" name="Preprocess files for SARTools" version="0.1.0"> | 1 <tool id="presartools" name="Preprocess files for SARTools" version="0.1.1"> |
| 2 <description>generate design/target file and archive for SARTools inputs</description> | 2 <description>generate design/target file and archive for SARTools inputs</description> |
| 3 <stdio> | 3 <stdio> |
| 4 <regex match="WARNING:galaxy.model:Datatype class not found" level="warning"/> | 4 <regex match="WARNING:galaxy.model:Datatype class not found" level="warning"/> |
| 5 </stdio> | 5 </stdio> |
| 6 <command interpreter="python"> | 6 <command><![CDATA[ |
| 7 pre_sartools.py | 7 python '$__tool_directory__/pre_sartools.py' |
| 8 --outfile=$outfile | 8 --outfile=$outfile |
| 9 --outarch=$outarch | 9 --outarch=$outarch |
| 10 #if $batch_condition.condition: | 10 #if $batch_condition.condition: |
| 11 --batch $batch_condition.condition | 11 --batch $batch_condition.condition |
| 12 #for $i, $input in enumerate ( $batch_condition.levels ): | 12 #for $i, $input in enumerate ( $batch_condition.levels ): |
| 21 --inputs "${input.level_name}" "${input_rep.count_data}" "${input_rep.label}" | 21 --inputs "${input.level_name}" "${input_rep.count_data}" "${input_rep.label}" |
| 22 #end for | 22 #end for |
| 23 #end for | 23 #end for |
| 24 #end if | 24 #end if |
| 25 | 25 |
| 26 </command> | 26 ]]></command> |
| 27 <inputs> | 27 <inputs> |
| 28 <conditional name="batch_condition"> | 28 <conditional name="batch_condition"> |
| 29 <param name="condition" type="boolean" checked="false" truevalue="batch" falsevalue="NULL" label="Add a blocking factor" help="Adjustment variable to use as a batch effect (default no)."/> | 29 <param name="condition" type="boolean" checked="false" truevalue="batch" falsevalue="NULL" label="Add a blocking factor" help="Adjustment variable to use as a batch effect (default no)."/> |
| 30 <when value="NULL"> | 30 <when value="NULL"> |
| 31 <repeat name="levels" title="Group" min="2"> | 31 <repeat name="levels" title="Group" min="2"> |
| 99 <param name="levels_1|level_name" value="group2"/> | 99 <param name="levels_1|level_name" value="group2"/> |
| 100 <param name="levels_1|rep_counts_0|count_data" value="group2_count1.txt"/> | 100 <param name="levels_1|rep_counts_0|count_data" value="group2_count1.txt"/> |
| 101 <param name="levels_1|rep_counts_0|label" value="group2_rep1"/> | 101 <param name="levels_1|rep_counts_0|label" value="group2_rep1"/> |
| 102 <param name="levels_1|rep_counts_1|count_data" value="group2_count2.txt"/> | 102 <param name="levels_1|rep_counts_1|count_data" value="group2_count2.txt"/> |
| 103 <param name="levels_1|rep_counts_1|label" value="group2_rep2"/> | 103 <param name="levels_1|rep_counts_1|label" value="group2_rep2"/> |
| 104 <output name="outfile" file="test_output_target.html"/> | 104 <output name="outfile" file="test_output_target.html" compare="re_match"/> |
| 105 </test> | 105 </test> |
| 106 </tests> | 106 </tests> |
| 107 <help> | 107 <help> |
| 108 ----------- | 108 ----------- |
| 109 Description | 109 Description |
| 113 * The count file must be outcoming from htseq-count or RSEM | 113 * The count file must be outcoming from htseq-count or RSEM |
| 114 | 114 |
| 115 * In input of SARTools, don't change the "factor of interest", by default is group but you need to change the "Reference biological condition" in order to correspond to one name of the groups. | 115 * In input of SARTools, don't change the "factor of interest", by default is group but you need to change the "Reference biological condition" in order to correspond to one name of the groups. |
| 116 * If you add a blocking factor, you need to specify it in "Advanced Parameters" of SARTools | 116 * If you add a blocking factor, you need to specify it in "Advanced Parameters" of SARTools |
| 117 </help> | 117 </help> |
| 118 <citations> | |
| 119 <citation type="doi">10.1371/journal.pone.0157022</citation> | |
| 120 </citations> | |
| 118 </tool> | 121 </tool> |