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comparison freyja_demix.xml @ 1:c0a0e79d7196 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
author iuc
date Fri, 07 Jul 2023 05:51:15 +0000
parents fc6252e78d5b
children
comparison
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0:fc6252e78d5b 1:c0a0e79d7196
28 #end if 28 #end if
29 #if $meta 29 #if $meta
30 --meta '$meta' 30 --meta '$meta'
31 #end if 31 #end if
32 $confirmedonly 32 $confirmedonly
33 $wgisaid
33 @CUSTOM_BARCODES_COMMAND@ 34 @CUSTOM_BARCODES_COMMAND@
34 --covcut $depth_cutoff 35 --covcut $depth_cutoff
35 --output abundances_raw.tsv && 36 --output abundances_raw.tsv &&
36 sed 's/$in_file/$sn/' abundances_raw.tsv > abundances.tsv 37 sed 's/$in_file/$sn/' abundances_raw.tsv > abundances.tsv
37 ]]></command> 38 ]]></command>
71 </conditional> 72 </conditional>
72 <conditional name="sample_name"> 73 <conditional name="sample_name">
73 <param name="source" value="manual"/> 74 <param name="source" value="manual"/>
74 <param name="name" value="samplename"/> 75 <param name="name" value="samplename"/>
75 </conditional> 76 </conditional>
76 <output name="abundances" ftype="tabular"> 77 <output name="abundances">
77 <assert_contents> 78 <assert_contents>
78 <has_text text="samplename"/> 79 <has_n_columns n="2" />
80 <has_text text="AY.48"/>
79 </assert_contents> 81 </assert_contents>
80 </output> 82 </output>
81 </test> 83 </test>
82 <!-- Test 02: autoname sample --> 84 <!-- Test 02: autoname sample -->
83 <test expect_num_outputs="1"> 85 <test expect_num_outputs="1">
87 <param name="choice" value="repo"/> 89 <param name="choice" value="repo"/>
88 </conditional> 90 </conditional>
89 <conditional name="sample_name"> 91 <conditional name="sample_name">
90 <param name="source" value="auto"/> 92 <param name="source" value="auto"/>
91 </conditional> 93 </conditional>
92 <output name="abundances" ftype="tabular"> 94 <output name="abundances">
93 <assert_contents> 95 <assert_contents>
94 <has_text text="summarized"/> 96 <has_n_columns n="2" />
97 <has_text text="AY.48"/>
95 </assert_contents> 98 </assert_contents>
96 </output> 99 </output>
97 </test> 100 </test>
98 </tests> 101 </tests>
99 <help><![CDATA[ 102 <help><![CDATA[