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comparison multiqc.xml @ 15:3d93dd18d9f8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
author iuc
date Sat, 18 Jan 2020 03:08:54 -0500
parents 161f4383df15
children bf675f34b056
comparison
equal deleted inserted replaced
14:b2f1f75d49c4 15:3d93dd18d9f8
1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@"> 1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1">
2 <description>aggregate results from bioinformatics analyses into a single report</description> 2 <description>aggregate results from bioinformatics analyses into a single report</description>
3 <macros> 3 <macros>
4 <token name="@WRAPPER_VERSION@">1.7</token> 4 <token name="@WRAPPER_VERSION@">1.7</token>
5 <token name="@ESCAPE_IDENTIFIER@"> 5 <token name="@ESCAPE_IDENTIFIER@">
6 <![CDATA[ 6 <![CDATA[
453 --title "$title" 453 --title "$title"
454 #end if 454 #end if
455 #if str($comment) 455 #if str($comment)
456 --comment "$comment" 456 --comment "$comment"
457 #end if 457 #end if
458
459 $flat
458 460
459 #if $configfile == "T" 461 #if $configfile == "T"
460 --config '$multiqc_config' 462 --config '$multiqc_config'
461 #end if 463 #end if
462 ]]></command> 464 ]]></command>
807 </when> 809 </when>
808 </conditional> 810 </conditional>
809 </repeat> 811 </repeat>
810 <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"/> 812 <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"/>
811 <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/> 813 <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/>
812 <param name="saveLog" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/> 814 <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="False" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/>
813 <param name="saveLog" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/> 815 <param name="saveLog" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/>
814 </inputs> 816 </inputs>
815 <outputs> 817 <outputs>
816 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" /> 818 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" />
817 <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log"> 819 <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log">
818 <filter>saveLog</filter> 820 <filter>saveLog</filter>
819 </data> 821 </data>
820 <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats"> 822 <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats">
821 <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" /> 823 <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
824 </collection>
825 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
826 <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+_plot_.+)\.txt" format="tabular" directory="report_data" />
822 </collection> 827 </collection>
823 </outputs> 828 </outputs>
824 <tests> 829 <tests>
825 <test> 830 <test>
826 <repeat name="results"> 831 <repeat name="results">
1219 <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab" /> 1224 <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab" />
1220 </conditional> 1225 </conditional>
1221 </repeat> 1226 </repeat>
1222 <output name="html_report" file="report_manual_custom_content.html" compare="sim_size"/> 1227 <output name="html_report" file="report_manual_custom_content.html" compare="sim_size"/>
1223 </test> 1228 </test>
1229 <test>
1230 <repeat name="results">
1231 <conditional name="software_cond">
1232 <param name="software" value="fastqc" />
1233 <repeat name="output">
1234 <param name="type" value="data"/>
1235 <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
1236 </repeat>
1237 </conditional>
1238 </repeat>
1239 <param name="title" value="Title of the report"/>
1240 <param name="comment" value="Commment for the report"/>
1241 <param name="flat" value="True"/>
1242 <output name="html_report">
1243 <assert_contents>
1244 <has_text text="Title of the report" />
1245 <has_text text="Commment for the report" />
1246 <has_text text="fastqc_seq_heatmap_key_t" />
1247 </assert_contents>
1248 </output>
1249 <output_collection name="plots" type="list">
1250 <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/>
1251 </output_collection>
1252 </test>
1224 </tests> 1253 </tests>
1225 <help><![CDATA[ 1254 <help><![CDATA[
1226 **What it does** 1255 **What it does**
1227 1256
1228 `MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools. 1257 `MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools.