Mercurial > repos > iuc > seqkit_fx2tab

changeset 7:6f3db0c7a725 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
author iuc
date Fri, 26 Sep 2025 16:47:22 +0000
parents 8eed2ffb2f6a
children 133c83f9bdc8
files macros.xml seqkit_fx2tab.xml test-data/fx2tab_output4.tabular test-data/grep_output1.fasta.gz test-data/grep_output2.fasta.gz test-data/grep_output3.fastq.gz test-data/grep_output4.fasta.gz test-data/grep_pattern.fasta test-data/hairpin.fa.gz test-data/reads_1.fq.gz test-data/reads_2.fq.gz test-data/stats_output1.tabular test-data/stats_output2.tabular
diffstat 13 files changed, 48 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Mar 17 09:50:29 2025 +0000
+++ b/macros.xml	Fri Sep 26 16:47:22 2025 +0000
@@ -1,7 +1,8 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.10.0</token>
+    <token name="@TOOL_VERSION@">2.10.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">20.09</token>
+    <token name="@PROFILE@">24.0</token>
+    <token name="@FASTQ_TYPES@">fasta,fasta.gz,fastqsanger,fastqsanger.gz</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">seqkit</xref>
--- a/seqkit_fx2tab.xml	Mon Mar 17 09:50:29 2025 +0000
+++ b/seqkit_fx2tab.xml	Fri Sep 26 16:47:22 2025 +0000
@@ -15,6 +15,12 @@
 '${input_identifier}'
 $alphabet
 $avg_qual
+#if str($B) != 'None'
+    -B ${ str($B).replace(",","") }
+#end if
+#if str($C) != 'None'
+    -C ${ str($C).replace(",","") }
+#end if
 $gc
 $gc_skew
 $header_line
@@ -32,6 +38,20 @@
         <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
         <param argument="--alphabet" type="boolean" truevalue="--alphabet" falsevalue="" checked="false" label="Output alphabet letters?"/>
         <param argument="--avg_qual" type="boolean" truevalue="--avg-qual" falsevalue="" checked="false" label="Output average quality of the read?"/>
+        <param argument="-B" type="select" multiple="true" label="Append a precentage column of the selected bases">
+            <option value="A"></option>
+            <option value="G"></option>
+            <option value="C"></option>
+            <option value="T"></option>
+            <option value="N"></option>
+        </param>
+        <param argument="-C" type="select" multiple="true" label="Append a count column of the selected bases">
+            <option value="A"></option>
+            <option value="G"></option>
+            <option value="C"></option>
+            <option value="T"></option>
+            <option value="N"></option>
+        </param>
         <param argument="--gc" type="boolean" truevalue="--gc" falsevalue="" checked="false" label="Output GC content?"/>
         <param argument="--gc_skew" type="boolean" truevalue="--gc-skew" falsevalue="" checked="false" label="Output GC-Skew?"/>
         <param argument="--header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="false" label="Output header line?"/>
@@ -51,11 +71,11 @@
         </test>
         <test expect_num_outputs="1">
             <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
-            <param name="avg_qual" value="--avg-qual"/>
-            <param name="header_line" value="--header-line"/>
-            <param name="length" value="--length"/>
-            <param name="name" value="--name"/>
-            <param name="only_id" value="--only-id"/>
+            <param name="avg_qual" value="true"/>
+            <param name="header_line" value="true"/>
+            <param name="length" value="true"/>
+            <param name="name" value="true"/>
+            <param name="only_id" value="true"/>
             <output name="output" file="fx2tab_output2.tabular" ftype="tabular"/>
         </test>
         <test expect_num_outputs="1">
@@ -64,16 +84,18 @@
         </test>
         <test expect_num_outputs="1">
             <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
-            <param name="alphabet" value="--alphabet"/>
-            <param name="avg_qual" value="--avg-qual"/>
-            <param name="gc" value="--gc"/>
-            <param name="gc_skew" value="--gc-skew"/>
-            <param name="header_line" value="--header-line"/>
-            <param name="length" value="--length"/>
-            <param name="name" value="--name"/>
-            <param name="no_qual" value="--no-qual"/>
-            <param name="only_id" value="--only-id"/>
-            <param name="seq_hash" value="--seq-hash"/>
+            <param name="alphabet" value="true"/>
+            <param name="avg_qual" value="true"/>
+            <param name="B" value="A,T"/>
+            <param name="C" value="A"/>
+            <param name="gc" value="true"/>
+            <param name="gc_skew" value="true"/>
+            <param name="header_line" value="true"/>
+            <param name="length" value="true"/>
+            <param name="name" value="true"/>
+            <param name="no_qual" value="true"/>
+            <param name="only_id" value="true"/>
+            <param name="seq_hash" value="true"/>
             <output name="output" file="fx2tab_output4.tabular" ftype="tabular"/>
         </test>
     </tests>
--- a/test-data/fx2tab_output4.tabular	Mon Mar 17 09:50:29 2025 +0000
+++ b/test-data/fx2tab_output4.tabular	Fri Sep 26 16:47:22 2025 +0000
@@ -1,4 +1,4 @@
-#id	length	GC	GC-Skew	alphabet	avg.qual	seq.hash
-ENA|AB011145|AB011145.1	4796	38.47	11.65	ACGT	0.00	c19cf05cadbdbc26e22efc2201acfcec
-ENA|M10051|M10051.1	4723	55.24	0.50	ACGT	0.00	4f6bbf79e427ef90b6f31de5023ad241
-ENA|BC112106|BC112106.1	1213	58.78	-15.01	ACGT	0.00	3b099f7df389373bb7e3269efc819599
+#id	length	GC	GC-Skew	A	AT	alphabet	avg.qual	seq.hash
+ENA|AB011145|AB011145.1	4796	38.47	11.65	1545	61.53	ACGT	0.00	c19cf05cadbdbc26e22efc2201acfcec
+ENA|M10051|M10051.1	4723	55.24	0.50	1068	44.76	ACGT	0.00	4f6bbf79e427ef90b6f31de5023ad241
+ENA|BC112106|BC112106.1	1213	58.78	-15.01	233	41.22	ACGT	0.00	3b099f7df389373bb7e3269efc819599
Binary file test-data/grep_output1.fasta.gz has changed
Binary file test-data/grep_output2.fasta.gz has changed
Binary file test-data/grep_output3.fastq.gz has changed
Binary file test-data/grep_output4.fasta.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/grep_pattern.fasta	Fri Sep 26 16:47:22 2025 +0000
@@ -0,0 +1,2 @@
+ENA|AB011145|AB011145.1
+ENA|BC112106|BC112106.1
Binary file test-data/hairpin.fa.gz has changed
Binary file test-data/reads_1.fq.gz has changed
Binary file test-data/reads_2.fq.gz has changed
--- a/test-data/stats_output1.tabular	Mon Mar 17 09:50:29 2025 +0000
+++ b/test-data/stats_output1.tabular	Fri Sep 26 16:47:22 2025 +0000
@@ -1,2 +1,2 @@
 file	format	type	num_seqs	sum_len	min_len	avg_len	max_len	Q1	Q2	Q3	sum_gap	N50	N50_num	Q20(%)	Q30(%)	AvgQual	GC(%)	sum_n
-input1_fastq_gz	FASTQ	DNA	5	505	101	101.0	101	101.0	101.0	101.0	0	101	1	98.02	89.31	25.93	35.45	0
+input1_fastq_gz	FASTQ	DNA	5	505	101	101.0	101	101	101	101	0	101	1	98	89	25.93	35.45	0
--- a/test-data/stats_output2.tabular	Mon Mar 17 09:50:29 2025 +0000
+++ b/test-data/stats_output2.tabular	Fri Sep 26 16:47:22 2025 +0000
@@ -1,2 +1,2 @@
 file	format	type	num_seqs	sum_len	min_len	avg_len	max_len	Q1	Q2	Q3	sum_gap	N50	N50_num	Q20(%)	Q30(%)	AvgQual	GC(%)	sum_n
-input1_fasta_gz	FASTA	DNA	3	10732	1213	3577.3	4796	2968.0	4723.0	4759.5	0	4723	2	0.00	0.00	0.00	48.15	0
+input1_fasta_gz	FASTA	DNA	3	10732	1213	3577.3	4796	2968	4723	4760	0	4723	2	0	0	0.00	48.15	0