Repository 'fastplong'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/fastplong

Changeset 2:8d31d5da8662 (2025-07-19)
Previous changeset 1:1d34936d4497 (2025-06-02) Next changeset 3:23f75f8716cf (2025-08-15)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastplong commit 8ff99077479b995d644277bacb038478f870409f
modified:
fastplong.xml
b
diff -r 1d34936d4497 -r 8d31d5da8662 fastplong.xml
--- a/fastplong.xml Mon Jun 02 10:09:14 2025 +0000
+++ b/fastplong.xml Sat Jul 19 08:24:14 2025 +0000
[
b'@@ -1,4 +1,4 @@\n-<tool id="fastplong" name="Fastplong" version="@TOOL_VERSION@+galaxy0" profile="23.2" license="MIT">\n+<tool id="fastplong" name="Fastplong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="MIT">\n     <description>Filter and trim long reads</description>\n     <creator>\n         <organization name="Masaryk University" url="https://www.muni.cz/"/>\n@@ -6,163 +6,430 @@\n     </creator>\n     <macros>\n         <token name="@TOOL_VERSION@">0.3.0</token>\n+        <token name="@VERSION_SUFFIX@">1</token>\n     </macros>\n     <requirements>\n         <requirement type="package" version="@TOOL_VERSION@">fastplong</requirement>\n     </requirements>\n     <command detect_errors="exit_code">\n-        <![CDATA[\n-        fastplong \n-        --thread \\${GALAXY_SLOTS:-1}\n-        --report_title \'fastplong report for $in\'\n-        --in \'$in\'\n-        --out \'$output\'\n-        #if $reads_to_process: \n-            --reads_to_process \'$reads_to_process\'\n-        #end if\n-        $disable_quality_filtering\n-        $disable_adapter_trimming\n-        #if $start_adapter:\n-            --start_adapter \'$start_adapter\'\n-        #end if\n-        #if $end_adapter:\n-            --end_adapter \'$end_adapter\'\n-        #end if\n-        #if $adapter_fasta:\n-            --adapter_fasta \'$adapter_fasta\'\n-        #end if\n-        #if $distance_threshold:\n-            --distance_threshold \'$distance_threshold\'\n-        #end if\n-        #if $trimming_extension:\n-            --trimming_extension \'$trimming_extension\'\n-        #end if\n-        #if $trim_front:\n-            --trim_front \'$trim_front\'\n-        #end if\n-        #if $trim_tail:\n-            --trim_tail \'$trim_tail\'\n-        #end if\n-        $trim_poly_x\n-        #if $poly_x_min_len:\n-            --poly_x_min_len \'$poly_x_min_len\'\n-        #end if\n-        $cut_front\n-        $cut_tail\n-        #if $cut_window_size:\n-            --cut_window_size \'$cut_window_size\'\n-        #end if\n-        #if $cut_mean_quality:\n-            --cut_mean_quality \'$cut_mean_quality\'\n-        #end if\n-        #if $cut_front_window_size:\n-            --cut_front_window_size \'$cut_front_window_size\'\n-        #end if\n-        #if $cut_front_mean_quality:\n-            --cut_front_mean_quality \'$cut_front_mean_quality\'\n-        #end if\n-        #if $cut_tail_window_size:\n-            --cut_tail_window_size \'$cut_tail_window_size\'\n-        #end if\n-        #if $cut_tail_mean_quality:\n-            --cut_tail_mean_quality \'$cut_tail_mean_quality\'\n-        #end if\n-        #if $qualified_quality_phred:\n-            --qualified_quality_phred \'$qualified_quality_phred\'\n-        #end if\n-        #if $unqualified_percent_limit:\n-            --unqualified_percent_limit \'$unqualified_percent_limit\'\n-        #end if\n-        #if $n_base_limit:\n-            --n_base_limit \'$n_base_limit\'\n-        #end if\n-        #if $mean_qual:\n-            --mean_qual \'$mean_qual\'\n-        #end if\n-        $disable_length_filtering:\n-        #if $length_required:\n-            --length_required \'$length_required\'\n-        #end if\n-        #if $length_limit:\n-            --length_limit \'$length_limit\'\n-        #end if\n-        $low_complexity_filter:\n-        #if $complexity_threshold:\n-            --complexity_threshold \'$complexity_threshold\'\n-        #end if\n-        $failed_out failed_reads.fastq\n-        ]]>\n+ <![CDATA[\n+ #import re\n+\n+ ## Link input files\n+\n+ #set ext = \'.fastq\'\n+\n+ #if $in.is_of_type(\'fastq.gz\')\n+    #set ext = \'.fastq.gz\'\n+ #end if\n+\n+ #set $in_name = re.sub(\'[^\\w\\-\\s]\', \'_\', str($in.element_identifier)) + $ext\n+ ln -sf \'$in\' \'$in_name\' &&\n+\n+ ## Run fastplong\n+ fastplong \n+ \n+ --thread \\${GALAXY_SLOTS:-1}\n+ --report_title \'fastplong report for $in_name\'\n+ --in \'$in_name\'\n+ --out long${ext}\n+\n+ #if $reads_to_process: \n+    --reads_to_process \'$reads_to_process\'\n+ #end if\n+\n+ ## Adapter Trimming Options\n+ \n+ #if $adapter_trimming_options.adapter_trim.disable_adapter_trimming == \'yes\'\n+    --disable_ada'..b'           <param name="in" value="input.fastq"/>\n-            <output name="output" file="output.fastq"/>\n+            <output name="report_html">\n+                <assert_contents>\n+                    <has_text text="html"/>\n+                    <has_text text="fastplong report"/>\n+                </assert_contents>\n+            </output>\n         </test>\n         <test expect_num_outputs="3">\n             <param name="in" value="input.fastq"/>\n-            <param name="reads_to_process" value="3"/>\n-            <output name="output" file="output_reads_to_process.fastq"/>\n+            <section name="output_options">\n+                <param name="report_json" value="true"/>\n+            </section>\n+            <output name="out" file="output.fastq"/>\n+            <output name="report_json">\n+\t\t\t\t<assert_contents>\n+\t\t\t\t\t<has_text text=\'summary": {\'/>\n+\t\t\t\t\t<has_text text=\'fastplong_version": "@TOOL_VERSION@\'/>\n+\t\t\t\t</assert_contents>\n+            </output>\n         </test>\n-        <test expect_num_outputs="4">\n+        <test expect_num_outputs="2">\n+            <param name="in" value="input.fastq"/>\n+            <output name="out" file="output.fastq"/>\n+        </test>\n+        <test expect_num_outputs="2">\n             <param name="in" value="input.fastq"/>\n-            <param name="failed_out" value="true"/>\n-            <output name="failed_out_reads" value="output_failed_out.fastq"/>\n+            <param name="reads_to_process" value="3"/>\n+            <output name="out" file="output_reads_to_process.fastq"/>\n+        </test>\n+        <test expect_num_outputs="3">\n+            <param name="in" value="input.fastq"/>\n+            <section name="output_options">\n+                <param name="failed_out" value="true"/>\n+            </section>\n+            <output name="failed_out" value="output_failed_out.fastq"/>\n         </test>\n     </tests>\n-    <help>\n-    **Fastplong: Filter and trim long reads**\n+    <help><![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+fastplong_ is a tool designed to provide fast all-in-one preprocessing for long reads FASTQ files. This tool is developed in C++ with multithreading supported to\n+afford high performance.\n+\n+*Features*\n+\n+1. Filter out bad reads (too low quality, too short, or too many N...)\n \n-        This tool wraps the `fastplong` command-line tool to allow filtering and trimming of long reads in FASTQ format.\n+2. Cut low quality bases for per read in its 5\' and 3\' by evaluating the mean quality from a sliding window (like Trimmomatic but faster)\n+\n+3. Trim all reads in front and tail\n+\n+4. Cut adapters. Adapter sequences can be automatically detected, which means you don\'t have to input the adapter sequences to trim them.\n+\n+5. Trim polyX in 3\' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)\n+\n+6. Report JSON format result for further interpreting\n+\n+7. Visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative)\n+\n \n-    **Inputs**\n-    - A FASTQ file containing reads and optional parameters to control trimming, quality filtering, adapter detection, and more.\n+-----\n+\n+**Inputs**\n+\n+Single-end FASTQ or FASTQ.GZ long reads\n+\n+-----\n+\n+**Outputs**\n+\n+    * Processed reads\n \n-    **Outputs**\n-    - A filtered FASTQ file with trimmed reads, HTML and JSON report and an optional FASTQ file of failed reads.\n+Optionally, under **Output Options** you can choose to output\n+\n+    * HTML report (default is Yes)\n+    * JSON report (compatible with MultiQC)\n+    * Failed reads (default is No)\n \n-    For more information, see https://github.com/OpenGene/fastplong\n-    </help>\n+**More Information**\n+\n+- **Official Repository**: [GitHub - OpenGene/fastplong](https://github.com/OpenGene/fastplong)\n+\n+.. _fastplong: https://github.com/OpenGene/fastplong\n+\n+]]></help>\n     <citations>\n         <citation type="doi">10.1002/imt2.107</citation>\n         <citation type="doi">10.1093/bioinformatics/bty560</citation>\n'