Mercurial > repos > iuc > multiqc
comparison 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 |
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date | Mon, 02 Sep 2024 14:22:54 +0000 |
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23:abfd8a6544d7 | 24:f7e2f1eb3a16 |
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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> |