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comparison dada2_dada.xml @ 9:00f5005840fa draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 9bbc0898b9bbe73c7fc60ac162d80d749a7f97c1
author iuc
date Fri, 24 May 2024 11:41:58 +0000
parents 84fd33a60b35
children
comparison
equal deleted inserted replaced
8:2cfceb9f9b8e 9:00f5005840fa
60 ## special case: for 1 sample the dada_result is not a list of dada 60 ## special case: for 1 sample the dada_result is not a list of dada
61 ## objects but it is a dada object 61 ## objects but it is a dada object
62 #if $batch_cond.batch_select == "no": 62 #if $batch_cond.batch_select == "no":
63 #if len($batch_cond.derep) > 1: 63 #if len($batch_cond.derep) > 1:
64 for( id in names(dada_result) ){ 64 for( id in names(dada_result) ){
65 print(id)
66 print(dada_result[[id]])
65 saveRDS(dada_result[[id]], file=file.path("output" ,paste(id, "dada2_dada", sep="."))) 67 saveRDS(dada_result[[id]], file=file.path("output" ,paste(id, "dada2_dada", sep=".")))
66 } 68 }
67 #else 69 #else
68 #for $d in $batch_cond.derep: 70 #for $d in $batch_cond.derep:
71 print(dada_result)
69 saveRDS(dada_result, file=file.path("output" ,paste('$d.element_identifier', "dada2_dada", sep="."))) 72 saveRDS(dada_result, file=file.path("output" ,paste('$d.element_identifier', "dada2_dada", sep=".")))
70 #end for 73 #end for
71 #end if 74 #end if
72 #else 75 #else
76 print(dada_result)
73 saveRDS(dada_result, file='$dada') 77 saveRDS(dada_result, file='$dada')
74 #end if 78 #end if
75 ]]></configfile> 79 ]]></configfile>
76 </configfiles> 80 </configfiles>
77 <inputs> 81 <inputs>
114 <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" /> 118 <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" />
115 <output_collection name="data_collection" type="list"> 119 <output_collection name="data_collection" type="list">
116 <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> 120 <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
117 <element name="filterAndTrim_F3D141_R1.fq.gz" file="dada_F3D141_S207_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> 121 <element name="filterAndTrim_F3D141_R1.fq.gz" file="dada_F3D141_S207_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
118 </output_collection> 122 </output_collection>
123 <assert_stdout>
124 <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
125 </assert_stdout>
119 </test> 126 </test>
120 <!-- default, batch --> 127 <!-- default, batch -->
121 <test expect_num_outputs="1"> 128 <test expect_num_outputs="1">
122 <param name="batch_cond|batch_select" value="yes"/> 129 <param name="batch_cond|batch_select" value="yes"/>
123 <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" /> 130 <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />
124 <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" /> 131 <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" />
125 <output name="dada" value="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> 132 <output name="dada" value="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
133 <assert_stdout>
134 <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
135 </assert_stdout>
126 </test> 136 </test>
127 <!-- test non-default options --> 137 <!-- test non-default options -->
128 <test expect_num_outputs="1"> 138 <test expect_num_outputs="1">
129 <param name="batch_cond|batch_select" value="no"/> 139 <param name="batch_cond|batch_select" value="no"/>
130 <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" /> 140 <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />
131 <param name="batch_cond|pool" value="pseudo"/> 141 <param name="batch_cond|pool" value="pseudo"/>
132 <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" /> 142 <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" />
133 <output_collection name="data_collection" type="list"> 143 <output_collection name="data_collection" type="list">
134 <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> 144 <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
135 </output_collection> 145 </output_collection>
146 <assert_stdout>
147 <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
148 </assert_stdout>
136 </test> 149 </test>
137 </tests> 150 </tests>
138 <help><![CDATA[ 151 <help><![CDATA[
139 Description 152 Description
140 ........... 153 ...........