Mercurial > repos > iuc > filtlong

changeset 4:428fd2cee5d9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong commit 5875d08292df3ceac45962dcc1790a36de9dcf9a
author iuc
date Tue, 23 Sep 2025 16:33:00 +0000
parents e6d48d485920
children
files filtlong.xml macros.xml
diffstat 2 files changed, 66 insertions(+), 40 deletions(-) [+]
line wrap: on
line diff
--- a/filtlong.xml	Thu Feb 24 21:21:47 2022 +0000
+++ b/filtlong.xml	Tue Sep 23 16:33:00 2025 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools" />
     <expand macro="requirements"/>
     <version_command>filtlong --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -28,11 +29,11 @@
     #if $external_references.assembly:
         --assembly '$external_references.assembly'
     #end if
-    #if $external_references.illumina_1:
-        --illumina_1 '$external_references.illumina_1'
+    #if $external_references.short_1:
+        --short_1 '$external_references.short_1'
     #end if
-    #if $external_references.illumina_2:
-        --illumina_2 '$external_references.illumina_2'
+    #if $external_references.short_2:
+        --short_2 '$external_references.short_2'
     #end if
     --length_weight '$score_weights.length_weight'
     --mean_q_weight '$score_weights.mean_q_weight'
@@ -49,17 +50,23 @@
     <inputs>
         <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ" help="FASTQ of input reads"/>
         <section name="output_thresholds" title="Output thresholds">
-            <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/>
+            <param argument="--target_bases" type="text" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases (unit suffixes: k, kb, m, mb, g, gb).">
+                <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator>
+            </param>
             <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/>
-            <param argument="--max_length" type="integer" min="0" optional="True" label="Max. length" help="Maximum length threshold"/>
-            <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/>
+            <param argument="--max_length" type="text" min="0" optional="True" label="Max. length" help="Maximum length threshold (unit suffixes: k, kb, m, mb, g, gb)">
+                <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator>
+            </param>
+            <param argument="--min_length" type="text" min="0" optional="True" label="Min. length" help="Minimum length threshold (unit suffixes: k, kb, m, mb, g, gb)">
+                <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator>
+            </param>
             <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/>
             <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/>
         </section>
         <section name="external_references" title="External references">
             <param argument="--assembly" type="data" format="fasta,fasta.gz" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/>
-            <param argument="--illumina_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
-            <param argument="--illumina_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
+            <param argument="--short_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
+            <param argument="--short_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
         </section>
         <section name="score_weights" title="Score weights">
             <param argument="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/>
@@ -68,7 +75,9 @@
         </section>
         <section name="read_manipulation" title="Read manipulation">
             <param argument="--trim" type="boolean" checked="false" truevalue="--trim" falsevalue="" label="Trim non-k-mer-matching" help="Trim non-k-mer-matching bases from start/end of reads"/>
-            <param argument="--split" type="integer" min="0" optional="True" label="Split at nr. of bases" help="split reads at this many (or more) consecutive non-k-mer-matching bases"/>
+            <param argument="--split" type="text" min="0" optional="True" label="Split at nr. of bases" help="split reads at this many (or more) consecutive non-k-mer-matching bases">
+                <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator>
+            </param>
         </section>
         <section name="other" title="Other">
             <param argument="--window_size" type="integer" min="0" value="250" optional="True" label="Sliding window size" help="size of sliding window used when measuring window quality (default: 250)"/>
@@ -78,44 +87,43 @@
         <data name="outfile" format="fastqsanger" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
-            <param name="min_length" value="1000"/>
-            <param name="keep_percent" value="50"/>
-            <param name="target_bases" value="500000000"/>
+            <section name="output_thresholds">
+                <param name="min_length" value="1000"/>
+                <param name="keep_percent" value="50"/>
+                <param name="target_bases" value="500mb"/>
+            </section>
             <output name="outfile" ftype="fastqsanger" file="output.fastq"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
-            <param name="assembly" ftype="fasta.gz" value="test_reference.fasta.gz"/>
-            <param name="illumina_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/>
-            <param name="illumina_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/>
-            <param name="min_length" value="1000"/>
-            <param name="keep_percent" value="90"/>
-            <param name="target_bases" value="500000000"/>
-            <param name="trim" value="True"/>
-            <param name="split" value="500"/>
+            <section name="external_references">
+                <param name="assembly" ftype="fasta.gz" value="test_reference.fasta.gz"/>
+                <param name="short_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/>
+                <param name="short_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/>
+            </section>
+            <section name="output_thresholds">
+                <param name="min_length" value="1000"/>
+                <param name="keep_percent" value="90"/>
+                <param name="target_bases" value="500mb"/>
+            </section>
+            <section name="read_manipulation">
+                <param name="trim" value="True"/>
+                <param name="split" value="500"/>
+            </section>
             <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
-            <param name="max_length" value="5000"/>
+            <section name="output_thresholds">
+                <param name="max_length" value="5000"/>
+            </section>
             <output name="outfile" ftype="fastqsanger" file="output_max_length.fastq"/>
         </test>
     </tests>
     <help><![CDATA[
 Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
     ]]></help>
-    <citations>
-        <citation type="bibtex">
-            @misc{rrwick2017,
-                author = {Wick, Ryan},
-                year = {2017},
-                title = {Filtlong},
-                publisher = {GitHub},
-                journal = {GitHub repository},
-                url = {https://github.com/rrwick/Filtlong},
-            }
-        </citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>
--- a/macros.xml	Thu Feb 24 21:21:47 2022 +0000
+++ b/macros.xml	Tue Sep 23 16:33:00 2025 +0000
@@ -1,11 +1,29 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.2.1</token>
+    <token name="@TOOL_VERSION@">0.3.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">20.01</token>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">filtlong</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">filtlong</requirement>
         </requirements>
     </xml>
-</macros>
-
+     <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{rrwick2017,
+                    author = {Wick, Ryan},
+                    year = {2017},
+                    title = {Filtlong},
+                    publisher = {GitHub},
+                    journal = {GitHub repository},
+                    url = {https://github.com/rrwick/Filtlong},
+                }
+            </citation>
+        </citations>
+    </xml>
+</macros>
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