Mercurial > repos > iuc > multiqc
diff picard_plugin.xml @ 24:f7e2f1eb3a16 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
| author | iuc |
|---|---|
| date | Mon, 02 Sep 2024 14:22:54 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,119 @@ +<macros> + <token name="@PICARD_COMMAND@"><![CDATA[ + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #if str($repeat2.type) == "alignment_metrics" + #set $pattern = "picard.analysis.AlignmentSummaryMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "basedistributionbycycle" + #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "gcbias" + #set $pattern = "picard.analysis.GcBias" + @LN_2_FILES@ + #elif str($repeat2.type) == "hsmetrics" + #set $pattern = "picard.analysis.directed.HsMetrics" + @ @ + #elif str($repeat2.type) == "insertsize" + #set $pattern = "picard.analysis.InsertSizeMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "markdups" + #set $pattern = "MarkDuplicates" + @LN_2_FILES@ + #elif str($repeat2.type) == "oxogmetrics" + #set $pattern = "picard.analysis.CollectOxoGMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "pcr_metrics" + #set $pattern = "picard.analysis.directed.TargetedPcrMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "rnaseqmetrics" + #set $pattern = "Collect" + @LN_2_FILES@ + #elif str($repeat2.type) == "rrbs_metrics" + #set $pattern = "picard.analysis.RrbsSummaryMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "wgs_metrics" + #set $pattern = "picard.analysis.CollectWgsMetrics$WgsMetrics" + @LN_2_FILES@ + #end if + #end for + ]]></token> + <xml name="picard_form"> + <repeat name="output" title="Picard output" min="1"> + <param name="type" type="select" label="Type of Picard output?"> + <option value="alignment_metrics">Alignment metrics</option> + <option value="basedistributionbycycle">Base distribution by cycle</option> + <option value="gcbias">GC bias</option> + <option value="hsmetrics">HS Metrics</option> + <option value="insertsize">Insert size</option> + <option value="markdups">Markdups</option> + <option value="oxogmetrics">Oxog metrics</option> + <option value="pcr_metrics">PCR metrics</option> + <option value="rnaseqmetrics">RNA Seq metrics</option> + <option value="rrbs_metrics">RRBS metrics</option> + <option value="wgs_metrics">WGS metrics</option> + </param> + <param name="input" type="data" format="txt" multiple="true" label="Picard output"/> + </repeat> + </xml> + <xml name="picard_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="picard"/> + <repeat name="output"> + <param name="type" value="gcbias"/> + <param name="input" value="picard_collectGcBias.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="insertsize"/> + <param name="input" value="picard_CollectInsertSizeMetrics.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="markdups"/> + <param name="input" value="picard_MarkDuplicates.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="basedistributionbycycle"/> + <param name="input" value="picard_CollectBaseDistributionByCycle.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="rnaseqmetrics"/> + <param name="input" value="picard_CollectRnaSeqMetrics.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="alignment_metrics"/> + <param name="input" value="picard_CollectAlignmentSummaryMetrics.txt"/> + </repeat> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="picard_CollectRnaSeqMetrics_bam"/> + <has_text text="picard_alignment_readlength"/> + <has_text text="picard-rna-assignment"/> + <has_text text="picard-markduplicates"/> + <has_text text="picard-insertsize"/> + <has_text text="picard-gcbias"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="picard_CollectRnaSeqMetrics_bam"/> + <has_text text="InsertSizeMetrics_mqc_generalstats_picard_insertsizemetrics_summed_median"/> + <has_text text="picard_CollectRnaSeqMetrics_bam"/> + <has_text text="RnaSeqMetrics_mqc_generalstats_picard_rnaseqmetrics_PCT_MRNA_BASES"/> + <has_text text="NA"/> + <has_n_lines n="4"/> + <has_n_columns n="6"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="3"/> + </test> + </xml> +</macros>