Mercurial > repos > devteam > fastq_groomer

changeset 7:b8144dbbc1ba draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
author iuc
date Sun, 23 Nov 2025 17:48:36 +0000
parents 3213285ee5d2
children
files fastq_groomer.xml macros.xml
diffstat 2 files changed, 186 insertions(+), 116 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_groomer.xml	Fri Oct 04 10:33:13 2024 +0000
+++ b/fastq_groomer.xml	Sun Nov 23 17:48:36 2025 +0000
@@ -99,239 +99,295 @@
         <test>
             <param name="input_file" value="fastq_invalid-line3" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="basic" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="basic" />
+            </conditional>
             <output name="output_file" file="fastq_invalid-line3_fixed" />
         </test>
         <!-- Test fix-id by setting the option -->
         <test>
             <param name="input_file" value="fastq_invalid-line3" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="fix_id" value="--fix-id" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="fix_id" value="true" />
+            </conditional>
             <output name="output_file" file="fastq_invalid-line3_fixed" />
         </test>
         <!-- Test fix-id / option not set; expect failure -->
         <test expect_failure="true">
             <param name="input_file" value="fastq_invalid-line3" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="fix_id" value="--no-fix-id" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="fix_id" value="false" />
+            </conditional>
         </test>
         <!-- These tests include test files adapted from supplemental material in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. -->
         <!-- Test basic options -->
         <test>
             <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="basic" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="basic" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
             <param name="input_type" value="cssanger" />
-            <param name="options_type_selector" value="basic" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="basic" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
         </test>
         <test>
             <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
             <param name="input_type" value="illumina" />
-            <param name="options_type_selector" value="basic" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="basic" />
+            </conditional>
             <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
             <param name="input_type" value="solexa" />
-            <param name="options_type_selector" value="basic" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="basic" />
+            </conditional>
             <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_as_illumina.fastqillumina" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="basic" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="basic" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
         </test>
         <!-- Test grooming from illumina -->
         <test>
             <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
             <param name="input_type" value="illumina" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="illumina" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="illumina" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="illumina_full_range_original_illumina.fastqillumina" />
         </test>
         <test>
             <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
             <param name="input_type" value="illumina" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="sanger" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="sanger" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
             <param name="input_type" value="illumina" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="solexa" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="solexa" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="illumina_full_range_as_solexa.fastqsolexa" />
         </test>
         <test>
             <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
             <param name="input_type" value="illumina" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="cssanger" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="cssanger" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="illumina_full_range_as_cssanger.fastqcssanger" />
         </test>
         <!-- Test grooming from sanger -->
         <test>
             <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="sanger" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="sanger" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="illumina" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="illumina" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="solexa" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="solexa" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="cssanger" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="cssanger" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
         </test>
         <!-- Test grooming from solexa -->
         <test>
             <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
             <param name="input_type" value="solexa" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="solexa" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="solexa" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
         </test>
         <test>
             <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
             <param name="input_type" value="solexa" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="illumina" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="illumina" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="solexa_full_range_as_illumina.fastqillumina" />
         </test>
         <test>
             <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
             <param name="input_type" value="solexa" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="sanger" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="sanger" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
             <param name="input_type" value="solexa" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="cssanger" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="cssanger" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="solexa_full_range_as_cssanger.fastqcssanger" />
         </test>
         <!-- Test grooming from cssanger -->
         <test>
             <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
             <param name="input_type" value="cssanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="cssanger" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="cssanger" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
             <param name="input_type" value="cssanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="sanger" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="sanger" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
             <param name="input_type" value="cssanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="illumina" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="illumina" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
             <param name="input_type" value="cssanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="solexa" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="solexa" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_as_cssanger_adapter_base_with_quality_score.fastqcssanger_fake_score" ftype="fastq" />
             <param name="input_type" value="cssanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="cssanger" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="cssanger" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
         </test>
         <!-- Test fastq with line wrapping -->
         <test>
             <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="sanger" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="sanger" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="illumina" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="illumina" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="wrapping_as_illumina.fastqillumina" />
         </test>
         <test>
             <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="solexa" />
-            <param name="force_quality_encoding" value="None" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="solexa" />
+                <param name="force_quality_encoding" value="None" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="wrapping_as_solexa.fastqsolexa" />
         </test>
         <!-- Test forcing quality score encoding -->
@@ -339,60 +395,74 @@
         <test>
             <param name="input_file" value="sanger_full_range_as_decimal_sanger.fastqsanger" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="sanger" />
-            <param name="force_quality_encoding" value="ascii" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="sanger" />
+                <param name="force_quality_encoding" value="ascii" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="sanger" />
-            <param name="force_quality_encoding" value="decimal" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="sanger" />
+                <param name="force_quality_encoding" value="decimal" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_as_decimal_sanger.fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_as_tab_decimal_sanger.fastqsanger" ftype="fastq" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="sanger" />
-            <param name="force_quality_encoding" value="ascii" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="sanger" />
+                <param name="force_quality_encoding" value="ascii" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
         </test>
         <!-- Solexa, range -5 - 62 -->
         <test>
             <param name="input_file" value="solexa_full_range_as_decimal_solexa.fastqsolexa" ftype="fastq" />
             <param name="input_type" value="solexa" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="solexa" />
-            <param name="force_quality_encoding" value="ascii" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="solexa" />
+                <param name="force_quality_encoding" value="ascii" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
         </test>
         <test>
             <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
             <param name="input_type" value="solexa" />
-            <param name="options_type_selector" value="advanced" />
-            <param name="output_type" value="solexa" />
-            <param name="force_quality_encoding" value="decimal" />
-            <param name="summarize_input" value="summarize_input" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="advanced" />
+                <param name="output_type" value="solexa" />
+                <param name="force_quality_encoding" value="decimal" />
+                <param name="summarize_input" value="summarize_input" />
+            </conditional>
             <output name="output_file" file="solexa_full_range_as_decimal_solexa.fastqsolexa" />
         </test>
         <!-- compressed formats -->
         <test>
             <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastq.gz" />
             <param name="input_type" value="sanger" />
-            <param name="options_type_selector" value="basic" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="basic" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" decompress="true" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger.bz2" ftype="fastq.bz2" />
             <param name="input_type" value="cssanger" />
-            <param name="options_type_selector" value="basic" />
+            <conditional name="options_type">
+                <param name="options_type_selector" value="basic" />
+            </conditional>
             <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" decompress="true" />
         </test>
     </tests>
--- a/macros.xml	Fri Oct 04 10:33:13 2024 +0000
+++ b/macros.xml	Sun Nov 23 17:48:36 2025 +0000
@@ -1,11 +1,11 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.1.5</token>
-    <token name="@VERSION_SUFFIX@">2</token>
-    <token name="@PROFILE@">23.1</token>
+    <token name="@TOOL_VERSION@">1.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">24.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">galaxy_sequence_utils</requirement>
             <yield/>
         </requirements>
-    </xml>>
+    </xml>
 </macros>