Mercurial > repos > oinizan > frogs
diff preprocess.xml @ 27:646bee69560f draft
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
| author | oinizan |
|---|---|
| date | Wed, 30 Apr 2025 06:13:02 +0000 |
| parents | 48a1ff3045e2 |
| children | fce825ec2c84 |
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--- a/preprocess.xml Thu Apr 03 05:58:59 2025 +0000 +++ b/preprocess.xml Wed Apr 30 06:13:02 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="FROGS_preprocess" name="FROGS_1 Pre-process" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> +<tool id="FROGS_preprocess" name="FROGS_1 Pre-process" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="22.05"> <description>merging, denoising and dereplication</description> <macros> <import>macros.xml</import> @@ -9,79 +9,81 @@ <requirement type="package" version="2.10">cutadapt</requirement> </expand> <command detect_errors="exit_code"> - preprocess.py '$sequencer_type.sequencer_selected' - --output-dereplicated '$dereplicated_file' --output-count '$count_file' --summary '$summary_file' - @CPUS@ - --min-amplicon-size $sequencer_type.min_amplicon_size - --max-amplicon-size $sequencer_type.max_amplicon_size - #if $sequencer_type.sequencer_selected in ('illumina', 'longreads') - #if $sequencer_type.is_primer_in_seq.primer_choice == "true" - --five-prim-primer '$sequencer_type.is_primer_in_seq.five_prim_primer' - --three-prim-primer '$sequencer_type.is_primer_in_seq.three_prim_primer' - #else - --without-primers - #end if - #else - --five-prim-primer '$sequencer_type.five_prim_primer' - --three-prim-primer '$sequencer_type.three_prim_primer' - #end if - - #if $sequencer_type.input_type.input_type_selected == "archive" - --input-archive '$sequencer_type.input_type.archive_file' - #if $sequencer_type.sequencer_selected == "illumina" and $sequencer_type.input_type.archive_type.archive_type_selected == "already_merged" - --already-contiged - #elif $sequencer_type.sequencer_selected == "illumina" - --R1-size $sequencer_type.input_type.archive_type.R1_size - --R2-size $sequencer_type.input_type.archive_type.R2_size - --mismatch-rate $sequencer_type.input_type.archive_type.mismatch_rate - --merge-software $sequencer_type.input_type.archive_type.merge_software_type.merge_software - #if $sequencer_type.input_type.archive_type.merge_software_type.merge_software == "flash" - --expected-amplicon-size $sequencer_type.input_type.archive_type.merge_software_type.expected_amplicon_size + [<![CDATA[ + preprocess.py '$sequencer_type.sequencer_selected' + --output-dereplicated '$dereplicated_file' --output-count '$count_file' --summary '$summary_file' + @CPUS@ + --min-amplicon-size $sequencer_type.min_amplicon_size + --max-amplicon-size $sequencer_type.max_amplicon_size + #if $sequencer_type.sequencer_selected in ('illumina', 'longreads') + #if $sequencer_type.is_primer_in_seq.primer_choice == "true" + --five-prim-primer '$sequencer_type.is_primer_in_seq.five_prim_primer' + --three-prim-primer '$sequencer_type.is_primer_in_seq.three_prim_primer' + #else + --without-primers #end if - #if $sequencer_type.input_type.archive_type.keep_unmerged == "Yes" - --keep-unmerged - #end if + #else + --five-prim-primer '$sequencer_type.five_prim_primer' + --three-prim-primer '$sequencer_type.three_prim_primer' #end if - #else - #set $sep = ' ' - #if $sequencer_type.sequencer_selected == "illumina" - --samples-names - #for $current in $sequencer_type.input_type.files_by_samples_type.samples - $sep'${current.name.strip()}' - #end for - --input-R1 - #for $current in $sequencer_type.input_type.files_by_samples_type.samples - $sep'${current.R1_file}' - #end for - #if $sequencer_type.input_type.files_by_samples_type.files_by_samples_type_selected == "already_merged" + + #if $sequencer_type.input_type.input_type_selected == "archive" + --input-archive '$sequencer_type.input_type.archive_file' + #if $sequencer_type.sequencer_selected == "illumina" and $sequencer_type.input_type.archive_type.archive_type_selected == "already_merged" --already-contiged - #else - --input-R2 - #for $current in $sequencer_type.input_type.files_by_samples_type.samples - $sep'${current.R2_file}' - #end for - --R1-size $sequencer_type.input_type.files_by_samples_type.R1_size - --R2-size $sequencer_type.input_type.files_by_samples_type.R2_size - --mismatch-rate $sequencer_type.input_type.files_by_samples_type.mismatch_rate - --merge-software $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software - #if $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software == "flash" - --expected-amplicon-size $sequencer_type.input_type.files_by_samples_type.merge_software_type.expected_amplicon_size + #elif $sequencer_type.sequencer_selected == "illumina" + --R1-size $sequencer_type.input_type.archive_type.R1_size + --R2-size $sequencer_type.input_type.archive_type.R2_size + --mismatch-rate $sequencer_type.input_type.archive_type.mismatch_rate + --merge-software $sequencer_type.input_type.archive_type.merge_software_type.merge_software + #if $sequencer_type.input_type.archive_type.merge_software_type.merge_software == "flash" + --expected-amplicon-size $sequencer_type.input_type.archive_type.merge_software_type.expected_amplicon_size #end if - #if $sequencer_type.input_type.files_by_samples_type.keep_unmerged == "Yes" + #if $sequencer_type.input_type.archive_type.keep_unmerged == "Yes" --keep-unmerged #end if #end if #else - --samples-names - #for $current in $sequencer_type.input_type.samples - $sep'${current.name.strip()}' - #end for - --input-R1 - #for $current in $sequencer_type.input_type.samples - $sep'${current.R1_file}' - #end for + #set $sep = ' ' + #if $sequencer_type.sequencer_selected == "illumina" + --samples-names + #for $current in $sequencer_type.input_type.files_by_samples_type.samples + $sep'${current.name.strip()}' + #end for + --input-R1 + #for $current in $sequencer_type.input_type.files_by_samples_type.samples + $sep'${current.R1_file}' + #end for + #if $sequencer_type.input_type.files_by_samples_type.files_by_samples_type_selected == "already_merged" + --already-contiged + #else + --input-R2 + #for $current in $sequencer_type.input_type.files_by_samples_type.samples + $sep'${current.R2_file}' + #end for + --R1-size $sequencer_type.input_type.files_by_samples_type.R1_size + --R2-size $sequencer_type.input_type.files_by_samples_type.R2_size + --mismatch-rate $sequencer_type.input_type.files_by_samples_type.mismatch_rate + --merge-software $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software + #if $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software == "flash" + --expected-amplicon-size $sequencer_type.input_type.files_by_samples_type.merge_software_type.expected_amplicon_size + #end if + #if $sequencer_type.input_type.files_by_samples_type.keep_unmerged == "Yes" + --keep-unmerged + #end if + #end if + #else + --samples-names + #for $current in $sequencer_type.input_type.samples + $sep'${current.name.strip()}' + #end for + --input-R1 + #for $current in $sequencer_type.input_type.samples + $sep'${current.R1_file}' + #end for + #end if #end if - #end if + ]]> </command> <inputs> <conditional name="sequencer_type">