| Previous changeset 10:00e0347751b1 (2025-02-11) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 commit f65944aa0547c2fbe4b746cf443c85b2a76e9a48 |
|
modified:
dada2_filterAndTrim.xml macros.xml |
| b |
| diff -r 00e0347751b1 -r e8768ddeba32 dada2_filterAndTrim.xml --- a/dada2_filterAndTrim.xml Tue Feb 11 23:27:12 2025 +0000 +++ b/dada2_filterAndTrim.xml Sat Dec 20 14:14:13 2025 +0000 |
| [ |
| @@ -63,11 +63,6 @@ rev <- c(rev, '$paired_cond.reads.reverse') filt.fwd <- c(filt.fwd, '$paired_output.forward') filt.rev <- c(filt.rev, '$paired_output.reverse') -#else if $paired_cond.paired_select == "separate" - fwd <- c(fwd, '$paired_cond.reads') - rev <- c(rev, '$paired_cond.sdaer') - filt.fwd <- c(filt.fwd, '$output_fwd') - filt.rev <- c(filt.rev, '$output_rev') #else fwd <- c(fwd, '$paired_cond.reads') filt.fwd <- c(filt.fwd, '$output_single') @@ -122,12 +117,6 @@ <data name="output_single" format_source="paired_cond|reads" label="${tool.name} on ${on_string}: Reads" > <filter>paired_cond['paired_select'] == "single"</filter> </data> - <data name="output_fwd" format_source="paired_cond|reads" default_identifier_source="paired_cond|reads" label="${tool.name} on ${on_string}: Forward reads" > - <filter>paired_cond['paired_select'] == "separate"</filter> - </data> - <data name="output_rev" format_source="paired_cond|sdaer" default_identifier_source="paired_cond|sdaer" label="${tool.name} on ${on_string}: Reverse reads" > - <filter>paired_cond['paired_select'] == "separate"</filter> - </data> <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics"> <filter>output_statistics</filter> </data> @@ -156,17 +145,6 @@ </assert_contents> </output> </test> - <!-- paired data given separately --> - <test expect_num_outputs="3"> - <conditional name="paired_cond"> - <param name="paired_select" value="separate"/> - <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> - <param name="sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> - </conditional> - <output name="output_fwd" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> - <output name="output_rev" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" /> - <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular"/> - </test> <!-- single end data --> <test expect_num_outputs="1"> <conditional name="paired_cond"> @@ -177,7 +155,7 @@ <param name="rmlowcomplex" value="2" /> <param name="orientFwd" value="TACGG" /> <param name="output_statistics" value="FALSE" /> - <output name="output_fwd" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> + <output name="output_single" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> </test> <!-- single end data trimming --> <test expect_num_outputs="1"> @@ -190,7 +168,7 @@ <param name="trim|trimRight" value="2" /> <param name="trim|truncLen" value="2" /> <param name="output_statistics" value="FALSE" /> - <output name="output_fwd" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> + <output name="output_single" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> </test> <!-- single end data filtering --> <test expect_num_outputs="1"> @@ -204,7 +182,7 @@ <param name="filter|minQ" value="13" /> <param name="filter|maxEE" value="1" /> <param name="output_statistics" value="FALSE" /> - <output name="output_fwd" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> + <output name="output_single" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> </test> <!-- paired data w separate filters and trimmers for reverse --> <test expect_num_outputs="3"> |
| b |
| diff -r 00e0347751b1 -r e8768ddeba32 macros.xml --- a/macros.xml Tue Feb 11 23:27:12 2025 +0000 +++ b/macros.xml Sat Dec 20 14:14:13 2025 +0000 |
| [ |
| @@ -12,9 +12,9 @@ <xref type="bioconductor">dada2</xref> </xrefs> </xml> - <token name="@PROFILE@">23.2</token> + <token name="@PROFILE@">24.2</token> <token name="@TOOL_VERSION@">1.34.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="version_command"> <version_command><![CDATA[ @@ -80,17 +80,12 @@ <xml name="fastq_input" token_multiple="" token_collection_type="" token_argument_fwd="" token_argument_rev=""> <conditional name="paired_cond"> <param name="paired_select" type="select" label="Paired reads"> - <option value="paired">paired - in a data set pair</option> - <option value="separate">paired - in two separate data sets</option> + <option value="paired">paired</option> <option value="single">single</option> </param> <when value="paired"> <param name="reads" argument="@ARGUMENT_FWD@/@ARGUMENT_REV@" type="data_collection" collection_type="@COLLECTION_TYPE@" format="fastq,fastq.gz" label="Paired short read data"/> </when> - <when value="separate"> - <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Forward read data"/> - <param name="sdaer" argument="@ARGUMENT_REV@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Reverse read data"/> - </when> <when value="single"> <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Short read data"/> </when> |