| Previous changeset 14:ecb9f4854617 (2024-11-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889 |
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modified:
fastp.xml macros.xml |
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| diff -r ecb9f4854617 -r a626e8c0e1ba fastp.xml --- a/fastp.xml Mon Nov 11 14:53:41 2024 +0000 +++ b/fastp.xml Fri Nov 15 15:31:53 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy0" profile="23.1"> +<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy3" profile="23.1"> <description>fast all-in-one preprocessing for FASTQ files</description> <macros> <import>macros.xml</import> @@ -18,8 +18,6 @@ #if $single_paired.single_paired_selector == 'paired_collection' #if $single_paired.paired_input.forward.is_of_type('fastqsanger.gz') #set ext = '.fastqsanger.gz' - #elif $single_paired.paired_input.forward.is_of_type('fastqillumina.gz') - #set ext = '.fastqillumina.gz' #end if #set $in1 = $single_paired.paired_input.forward #set $in2 = $single_paired.paired_input.reverse @@ -32,8 +30,6 @@ #else #if $in1.is_of_type('fastqsanger.gz') #set ext = '.fastqsanger.gz' - #elif $in1.is_of_type('fastqillumina.gz') - #set ext = '.fastqillumina.gz' #end if #set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext @@ -45,8 +41,6 @@ #end if #end if -cp '$c1' galaxy.json && - ## Run fastp fastp @@ -54,10 +48,6 @@ --thread \${GALAXY_SLOTS:-1} --report_title 'fastp report for $in1_name' -#if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'): - --phred64 -#end if - -i '$in1_name' ## Merge reads @@ -231,40 +221,6 @@ mv second${ext} '${out2}' #end if ]]></command> - <configfiles> - <configfile name="c1"> - #set $ext1 = "fastqsanger" - #set $ext2 = "fastqsanger" - #if str($single_paired.single_paired_selector) == "single" - #if $in1.ext.endswith("gz") - #set $ext1 = "fastqsanger.gz" - #end if - #elif str($single_paired.single_paired_selector) == "paired" - #if $in1.ext.endswith("gz") - #set $ext1 = "fastqsanger.gz" - #end if - #if $in2.ext.endswith("gz") - #set $ext2 = "fastqsanger.gz" - #end if - #else - #if $paired_input.forward.ext.endswith("gz") - #set $ext1 = "fastqsanger.gz" - #end if - #if $paired_input.reverse.ext.endswith("gz") - #set $ext2 = "fastqsanger.gz" - #end if - #end if - { - "out1": {"ext": "$ext1"}, - "out2": {"ext": "$ext2"}, - "merged_reads": {"ext": "$ext1"}, - "unmerged_out1": {"ext": "$ext1"}, - "unmerged_out2": {"ext": "$ext2"}, - "unpaired1": {"ext": "$ext1"}, - "unpaired2": {"ext": "$ext2"} - } - </configfile> - </configfiles> <inputs> <conditional name="single_paired"> <param name="single_paired_selector" type="select" label="Single-end or paired reads"> @@ -288,7 +244,7 @@ <expand macro="global_trimming_options_paired" /> </when> <when value="paired_collection"> - <param name="paired_input" type="data_collection" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz" label="Select paired collection(s)" collection_type="paired"/> + <param name="paired_input" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Select paired collection(s)" collection_type="paired"/> <expand macro="merge_reads" /> <expand macro="adapter_trimming_options"> <expand macro="adapter_sequence" read_number="2"/> @@ -379,10 +335,10 @@ </inputs> <outputs> - <data name="out1" format="auto" label="${tool.name} on ${on_string}: Read 1 output"> + <data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 output"> <filter>single_paired['single_paired_selector'] in ["single", "paired"] and not single_paired['merge_reads']['merge']</filter> </data> - <data name="out2" format="auto" label="${tool.name} on ${on_string}: Read 2 output"> + <data name="out2" format_source="in2" label="${tool.name} on ${on_string}: Read 2 output"> <filter>single_paired['single_paired_selector'] == "paired" and not single_paired['merge_reads']['merge']</filter> </data> <collection name="output_paired_coll" type="paired" format_source="paired_input['forward']" label="${tool.name} on ${on_string}: Paired-end output"> @@ -394,20 +350,25 @@ <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON report"> <filter>output_options['report_json'] is True</filter> </data> - <data name="merged_reads" format="auto" label="${tool.name} on ${on_string}: Merged reads"> + <data name="merged_reads" format_source="in1" label="${tool.name} on ${on_string}: Merged reads"> <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge']</filter> + <expand macro="format_actions" read_number="1" forward_reverse="forward" /> </data> - <data name="unmerged_out1" format="auto" label="${tool.name} on ${on_string}: Unmerged filtered reads1"> + <data name="unmerged_out1" format_source="in1" label="${tool.name} on ${on_string}: Unmerged filtered reads1"> <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter> + <expand macro="format_actions" read_number="1" forward_reverse="forward" /> </data> - <data name="unmerged_out2" format="auto" label="${tool.name} on ${on_string}: Unmerged filtered reads2"> + <data name="unmerged_out2" format_source="in2" label="${tool.name} on ${on_string}: Unmerged filtered reads2"> <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter> + <expand macro="format_actions" read_number="2" forward_reverse="reverse" /> </data> - <data name="unpaired1" format="auto" label="${tool.name} on ${on_string}: Unmerged unfiltered reads1"> + <data name="unpaired1" format_source="in1" label="${tool.name} on ${on_string}: Unmerged unfiltered reads1"> <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter> + <expand macro="format_actions" read_number="1" forward_reverse="forward" /> </data> - <data name="unpaired2" format="auto" label="${tool.name} on ${on_string}: Unmerged unfiltered reads2"> + <data name="unpaired2" format_source="in2" label="${tool.name} on ${on_string}: Unmerged unfiltered reads2"> <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter> + <expand macro="format_actions" read_number="2" forward_reverse="reverse" /> </data> </outputs> @@ -664,7 +625,7 @@ **Inputs** -Single-end or Paired-end (compressed) fastqsagnger or fastqillumina files +Single-end or Paired-end (compressed) fastqsanger files ----- @@ -688,4 +649,4 @@ <citations> <citation type="doi">10.1101/274100</citation> </citations> -</tool> +</tool> \ No newline at end of file |
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| diff -r ecb9f4854617 -r a626e8c0e1ba macros.xml --- a/macros.xml Mon Nov 11 14:53:41 2024 +0000 +++ b/macros.xml Fri Nov 15 15:31:53 2024 +0000 |
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| @@ -61,11 +61,28 @@ </xml> <xml name="in" token_read_number="1" token_argument="-i"> - <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/> + <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastqsanger,fastqsanger.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/> </xml> <xml name="poly_g_min_len"> <param argument="--poly_g_min_len" type="integer" optional="true" label="PolyG minimum length" help="The minimum length to detect polyG in the read tail. 10 by default."/> </xml> -</macros> + + <xml name="format_actions" token_read_number="1" token_forward_reverse="forward"> + <actions> + <conditional name="single_paired.single_paired_selector"> + <when value="paired"> + <action type="format"> + <option type="from_param" name="single_paired.in@READ_NUMBER@" param_attribute="ext" /> + </action> + </when> + <when value="paired_collection"> + <action type="format"> + <option type="from_param" name="single_paired.paired_input" param_attribute="@FORWARD_REVERSE@.ext" /> + </action> + </when> + </conditional> + </actions> + </xml> +</macros> \ No newline at end of file |