| Previous changeset 3:02befcb391f5 (2017-05-15) Next changeset 5:1ee282794de3 (2022-03-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335" |
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modified:
prinseq.xml |
| b |
| diff -r 02befcb391f5 -r 654b3a274ed5 prinseq.xml --- a/prinseq.xml Mon May 15 11:03:57 2017 -0400 +++ b/prinseq.xml Wed Jul 07 09:22:27 2021 +0000 |
| [ |
| @@ -1,7 +1,10 @@ -<tool id="prinseq" name="PRINSEQ" version="0.20.4"> +<tool id="prinseq" name="PRINSEQ" version="@TOOL_VERSION+galaxy1"> <description>to process quality of sequences</description> + <macros> + <token name="@TOOL_VERSION">0.20.4</token> + </macros> <requirements> - <requirement type="package" version="0.20.4">prinseq</requirement> + <requirement type="package" version="@TOOL_VERSION">prinseq</requirement> </requirements> <stdio> @@ -34,7 +37,7 @@ #if $seq_type.input_singles.is_of_type('fastqillumina'): -phred64 #end if - #else: + #elif $seq_type.seq_type_opt == "paired": -fastq '$seq_type.input_mate1' -fastq2 '$seq_type.input_mate2' #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext: @@ -44,6 +47,12 @@ #if $seq_type.input_mate1.is_of_type('fastqillumina'): -phred64 #end if + #else + -fastq '$seq_type.input_collection.forward' + -fastq2 '$seq_type.input_collection.reverse' + #if $seq_type.input_collection.forward.is_of_type('fastqillumina'): + -phred64 + #end if #end if -out_good "tmp/good_sequences" @@ -225,6 +234,7 @@ <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?"> <option value="single" selected="true">Single-end</option> <option value="paired">Paired-end</option> + <option value="paired_collection">Paired Collection</option> </param> <when value="single"> <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." /> @@ -233,6 +243,9 @@ <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." /> <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." /> </when> + <when value="paired_collection"> + <param name="input_collection" type="data_collection" collection_type="paired" label="FASTQ collection" help="FASTQ data in a paired collection" /> + </when> </conditional> <conditional name="filter_treatments"> @@ -651,6 +664,18 @@ <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> + <collection name="good_sequences_collection" type="paired"> + <filter>seq_type['seq_type_opt'] == "paired_collection"</filter> + </collection> + + <collection name="singletons_collection" type="paired"> + <filter>seq_type['seq_type_opt'] == "paired_collection"</filter> + </collection> + + <collection name="rejected_sequences_collection" type="paired"> + <filter>seq_type['seq_type_opt'] == "paired_collection"</filter> + </collection> + <!--<data format="html" name="html_file" from_work_dir="stats_html.html" label="${tool.name} on ${on_string}: Summary" />--> </outputs> |