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comparison picard_plugin.xml @ 24:f7e2f1eb3a16 draft default tip

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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
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23:abfd8a6544d7 24:f7e2f1eb3a16
1 <macros>
2 <token name="@PICARD_COMMAND@"><![CDATA[
3 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
4 #if str($repeat2.type) == "alignment_metrics"
5 #set $pattern = "picard.analysis.AlignmentSummaryMetrics"
6 @LN_2_FILES@
7 #elif str($repeat2.type) == "basedistributionbycycle"
8 #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics"
9 @LN_2_FILES@
10 #elif str($repeat2.type) == "gcbias"
11 #set $pattern = "picard.analysis.GcBias"
12 @LN_2_FILES@
13 #elif str($repeat2.type) == "hsmetrics"
14 #set $pattern = "picard.analysis.directed.HsMetrics"
15 @ @
16 #elif str($repeat2.type) == "insertsize"
17 #set $pattern = "picard.analysis.InsertSizeMetrics"
18 @LN_2_FILES@
19 #elif str($repeat2.type) == "markdups"
20 #set $pattern = "MarkDuplicates"
21 @LN_2_FILES@
22 #elif str($repeat2.type) == "oxogmetrics"
23 #set $pattern = "picard.analysis.CollectOxoGMetrics"
24 @LN_2_FILES@
25 #elif str($repeat2.type) == "pcr_metrics"
26 #set $pattern = "picard.analysis.directed.TargetedPcrMetrics"
27 @LN_2_FILES@
28 #elif str($repeat2.type) == "rnaseqmetrics"
29 #set $pattern = "Collect"
30 @LN_2_FILES@
31 #elif str($repeat2.type) == "rrbs_metrics"
32 #set $pattern = "picard.analysis.RrbsSummaryMetrics"
33 @LN_2_FILES@
34 #elif str($repeat2.type) == "wgs_metrics"
35 #set $pattern = "picard.analysis.CollectWgsMetrics$WgsMetrics"
36 @LN_2_FILES@
37 #end if
38 #end for
39 ]]></token>
40 <xml name="picard_form">
41 <repeat name="output" title="Picard output" min="1">
42 <param name="type" type="select" label="Type of Picard output?">
43 <option value="alignment_metrics">Alignment metrics</option>
44 <option value="basedistributionbycycle">Base distribution by cycle</option>
45 <option value="gcbias">GC bias</option>
46 <option value="hsmetrics">HS Metrics</option>
47 <option value="insertsize">Insert size</option>
48 <option value="markdups">Markdups</option>
49 <option value="oxogmetrics">Oxog metrics</option>
50 <option value="pcr_metrics">PCR metrics</option>
51 <option value="rnaseqmetrics">RNA Seq metrics</option>
52 <option value="rrbs_metrics">RRBS metrics</option>
53 <option value="wgs_metrics">WGS metrics</option>
54 </param>
55 <param name="input" type="data" format="txt" multiple="true" label="Picard output"/>
56 </repeat>
57 </xml>
58 <xml name="picard_test">
59 <test expect_num_outputs="3">
60 <repeat name="results">
61 <conditional name="software_cond">
62 <param name="software" value="picard"/>
63 <repeat name="output">
64 <param name="type" value="gcbias"/>
65 <param name="input" value="picard_collectGcBias.txt"/>
66 </repeat>
67 <repeat name="output">
68 <param name="type" value="insertsize"/>
69 <param name="input" value="picard_CollectInsertSizeMetrics.txt"/>
70 </repeat>
71 <repeat name="output">
72 <param name="type" value="markdups"/>
73 <param name="input" value="picard_MarkDuplicates.txt"/>
74 </repeat>
75 <repeat name="output">
76 <param name="type" value="basedistributionbycycle"/>
77 <param name="input" value="picard_CollectBaseDistributionByCycle.txt"/>
78 </repeat>
79 <repeat name="output">
80 <param name="type" value="rnaseqmetrics"/>
81 <param name="input" value="picard_CollectRnaSeqMetrics.txt"/>
82 </repeat>
83 <repeat name="output">
84 <param name="type" value="alignment_metrics"/>
85 <param name="input" value="picard_CollectAlignmentSummaryMetrics.txt"/>
86 </repeat>
87 </conditional>
88 </repeat>
89 <param name="title" value="Title of the report"/>
90 <param name="comment" value="Commment for the report"/>
91 <param name="flat" value="true"/>
92 <param name="export" value="true"/>
93 <output name="html_report">
94 <assert_contents>
95 <has_text text="Title of the report"/>
96 <has_text text="Commment for the report"/>
97 <has_text text="picard_CollectRnaSeqMetrics_bam"/>
98 <has_text text="picard_alignment_readlength"/>
99 <has_text text="picard-rna-assignment"/>
100 <has_text text="picard-markduplicates"/>
101 <has_text text="picard-insertsize"/>
102 <has_text text="picard-gcbias"/>
103 </assert_contents>
104 </output>
105 <output name="stats">
106 <assert_contents>
107 <has_text text="picard_CollectRnaSeqMetrics_bam"/>
108 <has_text text="InsertSizeMetrics_mqc_generalstats_picard_insertsizemetrics_summed_median"/>
109 <has_text text="picard_CollectRnaSeqMetrics_bam"/>
110 <has_text text="RnaSeqMetrics_mqc_generalstats_picard_rnaseqmetrics_PCT_MRNA_BASES"/>
111 <has_text text="NA"/>
112 <has_n_lines n="4"/>
113 <has_n_columns n="6"/>
114 </assert_contents>
115 </output>
116 <output_collection name="plots" type="list" count="3"/>
117 </test>
118 </xml>
119 </macros>