Mercurial > repos > iuc > dimet_metabologram

comparison macros.xml @ 5:82fbf955bb0f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
author iuc
date Tue, 21 May 2024 13:42:49 +0000
parents 82fb756e71cf
children c7ff01bd331b
comparison
equal deleted inserted replaced
4:82fb756e71cf 5:82fbf955bb0f
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.2.4</token> 2 <token name="@TOOL_VERSION@">0.2.4</token>
3 <token name="@VERSION_SUFFIX@">1</token> 3 <token name="@VERSION_SUFFIX@">2</token>
4 <token name="@EXECUTABLE@">pca</token>
5 <xml name="requirements"> 4 <xml name="requirements">
6 <requirements> 5 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
8 </requirements> 7 </requirements>
9 </xml> 8 </xml>
488 <remove value="&quot;"/> 487 <remove value="&quot;"/>
489 <remove value="&apos;"/> 488 <remove value="&apos;"/>
490 </valid> 489 </valid>
491 </sanitizer> 490 </sanitizer>
492 </param> 491 </param>
493 <repeat name="factor_list" title="Conditions" default="2" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the first specified condition is the reference). You have to load a metadata file prior to have access to condition list"> 492 <repeat name="factor_list" title="Conditions" default="2" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the last specified condition is the reference). You have to load a metadata file prior to have access to condition list">
494 <param name="condition" label="Condition" type="select" optional="false" multiple="false"> 493 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
495 <options from_dataset="metadata_path"> 494 <options from_dataset="metadata_path">
496 <column name="condition" index="1"/> 495 <column name="condition" index="1"/>
497 <column name="value" index="1"/> 496 <column name="value" index="1"/>
498 <filter type="unique_value" name="condition" column="condition"/> 497 <filter type="unique_value" name="condition" column="condition"/>
550 </sanitizer> 549 </sanitizer>
551 </param> 550 </param>
552 </repeat> 551 </repeat>
553 </xml> 552 </xml>
554 <xml name="factor_list"> 553 <xml name="factor_list">
555 <repeat name="factor_list" title="Conditions" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the first specified condition is the reference). You have to load a metadata file prior to have access to condition list"> 554 <repeat name="factor_list" title="Conditions" min="2" max="2" help="Specify conditions to be taken into account from metadata file (for each comparison, the last specified condition is the reference). You have to load a metadata file prior to have access to condition list">
556 <param name="condition" label="Condition" type="select" optional="false" multiple="false"> 555 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
557 <options from_dataset="metadata_path"> 556 <options from_dataset="metadata_path">
558 <column name="condition" index="1"/> 557 <column name="condition" index="1"/>
559 <column name="value" index="1"/> 558 <column name="value" index="1"/>
560 <filter type="unique_value" name="condition" column="condition"/> 559 <filter type="unique_value" name="condition" column="condition"/>
613 ln -s '$metadata_path' data/metadata.csv && 612 ln -s '$metadata_path' data/metadata.csv &&
614 #end if 613 #end if
615 #if $abundance_file: 614 #if $abundance_file:
616 ln -s '$abundance_file' data/abundance.csv && 615 ln -s '$abundance_file' data/abundance.csv &&
617 #end if 616 #end if
617 #set $axisx = "condition"
618 #if str( $output_options.bar_color ) == "condition":
619 #set $axisx = "timepoint"
620 #end if
621
618 ]]></token> 622 ]]></token>
619 <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[ 623 <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[
620 624
621 mkdir -p data && 625 mkdir -p data &&
622 626