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comparison multiqc.xml @ 17:5e33b465d8d5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
author iuc
date Fri, 09 Oct 2020 14:56:59 +0000
parents bf675f34b056
children c19b16e5729c
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16:bf675f34b056 17:5e33b465d8d5
1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy0"> 1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy1">
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@">1.8</token> 4 <token name="@WRAPPER_VERSION@">1.8</token>
5 <token name="@ESCAPE_IDENTIFIER@"> 5 <token name="@ESCAPE_IDENTIFIER@">
6 <![CDATA[ 6 <![CDATA[
113 ln -s '$file' '$file_path' && 113 ln -s '$file' '$file_path' &&
114 #end for 114 #end for
115 #end if 115 #end if
116 #end for 116 #end for
117 #elif str($repeat.software_cond.software) == "bowtie2" 117 #elif str($repeat.software_cond.software) == "bowtie2"
118 #set $pattern = "reads; of these:" 118 #set $pattern = "% overall alignment rate"
119 @LN_FILES@ 119 @LN_FILES@
120 #elif str($repeat.software_cond.software) == "busco" 120 #elif str($repeat.software_cond.software) == "busco"
121 ## Searches for files "short_summary_[samplename].txt" 121 ## Searches for files "short_summary_[samplename].txt"
122 #for $file in $repeat.software_cond.input 122 #for $file in $repeat.software_cond.input
123 @ESCAPE_IDENTIFIER@ 123 @ESCAPE_IDENTIFIER@
248 @LN_2_FILES@ 248 @LN_2_FILES@
249 #elif str($repeat2.type) == "insertsize" 249 #elif str($repeat2.type) == "insertsize"
250 #set $pattern = "picard.analysis.InsertSizeMetrics" 250 #set $pattern = "picard.analysis.InsertSizeMetrics"
251 @LN_2_FILES@ 251 @LN_2_FILES@
252 #elif str($repeat2.type) == "markdups" 252 #elif str($repeat2.type) == "markdups"
253 #set $pattern = "picard.sam.DuplicationMetrics" 253 #set $pattern = "MarkDuplicates"
254 @LN_2_FILES@ 254 @LN_2_FILES@
255 #elif str($repeat2.type) == "oxogmetrics" 255 #elif str($repeat2.type) == "oxogmetrics"
256 #set $pattern = "picard.analysis.CollectOxoGMetrics" 256 #set $pattern = "picard.analysis.CollectOxoGMetrics"
257 @LN_2_FILES@ 257 @LN_2_FILES@
258 #elif str($repeat2.type) == "pcr_metrics" 258 #elif str($repeat2.type) == "pcr_metrics"
1299 1299
1300 MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. This is done using the **Software name** dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC 1300 MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. This is done using the **Software name** dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC
1301 1301
1302 ---- 1302 ----
1303 1303
1304 The first integration of this tool was made by Cyril Monjeaud and Yvan Le Bras (`Enancio <http://enancio.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility). It is now maintained by the `Intergalactic Utilities Commission <https://galaxyproject.org/iuc>`_. 1304 The first integration of this tool was made by
1305 `@cmonjeau <https://github.com/cmonjeau>`_ and `@yvanlebras <https://github.com/yvanlebras>`_.
1306 It is now maintained by the `Intergalactic Utilities Commission <https://galaxyproject.org/iuc>`_.
1305 ]]></help> 1307 ]]></help>
1306 <citations> 1308 <citations>
1307 <citation type="doi">10.1093/bioinformatics/btw354</citation> 1309 <citation type="doi">10.1093/bioinformatics/btw354</citation>
1308 </citations> 1310 </citations>
1309 </tool> 1311 </tool>