| Previous changeset 8:2cfceb9f9b8e (2024-05-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 9bbc0898b9bbe73c7fc60ac162d80d749a7f97c1 |
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modified:
dada2_dada.xml macros.xml |
| b |
| diff -r 2cfceb9f9b8e -r 00f5005840fa dada2_dada.xml --- a/dada2_dada.xml Thu May 23 08:50:44 2024 +0000 +++ b/dada2_dada.xml Fri May 24 11:41:58 2024 +0000 |
| [ |
| @@ -62,14 +62,18 @@ #if $batch_cond.batch_select == "no": #if len($batch_cond.derep) > 1: for( id in names(dada_result) ){ + print(id) + print(dada_result[[id]]) saveRDS(dada_result[[id]], file=file.path("output" ,paste(id, "dada2_dada", sep="."))) } #else #for $d in $batch_cond.derep: + print(dada_result) saveRDS(dada_result, file=file.path("output" ,paste('$d.element_identifier', "dada2_dada", sep="."))) #end for #end if #else + print(dada_result) saveRDS(dada_result, file='$dada') #end if ]]></configfile> @@ -116,6 +120,9 @@ <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> <element name="filterAndTrim_F3D141_R1.fq.gz" file="dada_F3D141_S207_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> </output_collection> + <assert_stdout> + <has_line line="43 sequence variants were inferred from 379 input unique sequences."/> + </assert_stdout> </test> <!-- default, batch --> <test expect_num_outputs="1"> @@ -123,6 +130,9 @@ <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" /> <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" /> <output name="dada" value="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> + <assert_stdout> + <has_line line="43 sequence variants were inferred from 379 input unique sequences."/> + </assert_stdout> </test> <!-- test non-default options --> <test expect_num_outputs="1"> @@ -133,6 +143,9 @@ <output_collection name="data_collection" type="list"> <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> </output_collection> + <assert_stdout> + <has_line line="43 sequence variants were inferred from 379 input unique sequences."/> + </assert_stdout> </test> </tests> <help><![CDATA[ |
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| diff -r 2cfceb9f9b8e -r 00f5005840fa macros.xml --- a/macros.xml Thu May 23 08:50:44 2024 +0000 +++ b/macros.xml Fri May 24 11:41:58 2024 +0000 |
| [ |
| @@ -12,8 +12,8 @@ <xref type="bioconductor">dada2</xref> </xrefs> </xml> - <token name="@DADA2_VERSION@">1.28</token> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@DADA2_VERSION@">1.30.0</token> + <token name="@WRAPPER_VERSION@">0</token> <xml name="version_command"> <version_command><![CDATA[ |