From fa7d4d515f26d2bed5e205084694488ba0bc9213 Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Tue, 3 Dec 2024 13:28:47 +0100
Subject: [PATCH 1/4] Output restruction for fastk tool

---
 tools/fastk/fastk.xml             |  38 +++++++++++++-----------------
 tools/fastk/macros.xml            |   2 +-
 tools/fastk/test-data/test01.hist | Bin 0 -> 262164 bytes
 tools/fastk/test-data/test02.hist | Bin 0 -> 262164 bytes
 tools/fastk/test-data/test03.hist | Bin 0 -> 262164 bytes
 5 files changed, 18 insertions(+), 22 deletions(-)
 create mode 100644 tools/fastk/test-data/test01.hist
 create mode 100644 tools/fastk/test-data/test02.hist
 create mode 100644 tools/fastk/test-data/test03.hist

diff --git a/tools/fastk/fastk.xml b/tools/fastk/fastk.xml
index 5adb5fff316..407835ac548 100644
--- a/tools/fastk/fastk.xml
+++ b/tools/fastk/fastk.xml
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir -p outfiles/ktabfiles && 
+        mkdir -p ktabfiles && 
         #if $infile.is_of_type("fastq"):
             #set INPUTFILE="input.fastq"
         #elif $infile.is_of_type("fastq.gz"):
@@ -21,17 +21,17 @@
         #elif $sorted_table.sorted_table_option == 'yes_with_custom':
             -t$sorted_table_cutoff 
         #end if
-        -T\${GALAXY_SLOTS:-8} -Noutfiles/output -Poutfiles/ktabfiles
+        -T\${GALAXY_SLOTS:-8} -Noutput -Pktabfiles
         #if $sorted_table.sorted_table_option == 'yes_with_default':
-            && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_default} LIST > '$tabex_hist'
-            && cp outfiles/.*.ktab* outfiles/ktabfiles 
-            && cp outfiles/*.ktab outfiles/ktabfiles
+            && Tabex output.ktab -t${sorted_table.tabex_threshold_for_default} LIST > '$tabex_hist'
+            && cp .*.ktab* ktabfiles/ 
+            && cp  *.ktab ktabfiles/
         #elif $sorted_table.sorted_table_option == 'yes_with_custom':
-            && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_custom} LIST > '$tabex_hist'
-            && cp outfiles/.*.ktab* outfiles/ktabfiles 
-            && cp outfiles/*.ktab outfiles/ktabfiles
+            && Tabex output.ktab -t${sorted_table.tabex_threshold_for_custom} LIST > '$tabex_hist'
+            && cp *.ktab* ktabfiles/
+            && cp *.ktab ktabfiles/
         #end if
-        && tar -c -f fastk.tar ./outfiles/
+        && tar -cf fastk.tar ktabfiles/
     ]]></command>
     <inputs>
         <param name="infile" type="data" format="fasta,fasta.gz,fastq,fastq.gz,cram,unsorted.bam,sam" label="Input file"/>   
@@ -54,8 +54,8 @@
     </inputs>
     <outputs>
         <data name="fastk_out" format="tar" from_work_dir="fastk.tar" label="${tool.name} on ${on_string}: FastK files"/>
-        <data name="fastk_hist_out" format="fastk_hist" from_work_dir="outfiles/output.hist" label="${tool.name} on ${on_string}: FastK hist"/>
-        <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="outfiles/ktabfiles/output.ktab" label="${tool.name} on ${on_string}: FastK ktab">
+        <data name="fastk_hist_out" format="fastk_hist" from_work_dir="output.hist" label="${tool.name} on ${on_string}: FastK hist"/>
+        <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="ktabfiles/output.ktab" label="${tool.name} on ${on_string}: FastK ktab">
             <filter> sorted_table['sorted_table_option'] != 'no' </filter> 
         </data>
         <data name="tabex_hist" format="txt"  label="${tool.name} on ${on_string}: Tabex output">
@@ -66,11 +66,8 @@
     <!-- TEST 1 -->
         <test expect_num_outputs="2">
             <param name="infile" value="input01.fasta.gz"/>
-            <output name="fastk_out" ftype="tar">
-                <assert_contents>
-                    <has_archive_member path="./outfiles/output.hist"/>
-                </assert_contents>
-            </output>
+            <param name="kmer_size" value="40"/>
+            <output name="fastk_hist_out" file="test01.hist" ftype="fastk_hist"/>
         </test>
         <!-- TEST 2 -->
         <test expect_num_outputs="4">
@@ -78,10 +75,10 @@
             <conditional name="sorted_table">
                 <param name="sorted_table_option" value="yes_with_default"/>
             </conditional>
+            <output name="fastk_hist_out" file="test02.hist" ftype="fastk_hist"/>
             <output name="fastk_out" ftype="tar">
                 <assert_contents>
-                    <has_archive_member path="./outfiles/output.hist"/>
-                    <has_archive_member path="./outfiles/ktabfiles/output.ktab"/>
+                    <has_archive_member path="ktabfiles/output.ktab"/>
                 </assert_contents>
             </output>
             <output name="tabex_hist" file="test02.tabex.txt"/>
@@ -93,10 +90,10 @@
                 <param name="sorted_table_option" value="yes_with_custom"/>
                 <param name="sorted_table_cutoff" value="5"/>
             </conditional>
+            <output name="fastk_hist_out" file="test03.hist" ftype="fastk_hist"/>
             <output name="fastk_out" ftype="tar">
                 <assert_contents>
-                    <has_archive_member path="./outfiles/output.hist"/>
-                    <has_archive_member path="./outfiles/ktabfiles/output.ktab"/>
+                    <has_archive_member path="ktabfiles/output.ktab"/>
                 </assert_contents>
             </output>
             <output name="tabex_hist" file="test03.tabex.txt"/>
@@ -115,7 +112,6 @@
 
         3. A tar file comprising of hidden .ktab files that can be used for downstream FASTK tools.
 
-
     ]]></help>
     <expand macro="citations"/>
 </tool>
\ No newline at end of file
diff --git a/tools/fastk/macros.xml b/tools/fastk/macros.xml
index 156ff7bab2b..a838e7a4ca5 100644
--- a/tools/fastk/macros.xml
+++ b/tools/fastk/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.1.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xrefs>
       <xref type="bio.tools">fastk</xref>
     </xrefs>
diff --git a/tools/fastk/test-data/test01.hist b/tools/fastk/test-data/test01.hist
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diff --git a/tools/fastk/test-data/test03.hist b/tools/fastk/test-data/test03.hist
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From 0da60ea1717154718ed52c20919069c1b5b5607a Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Wed, 4 Dec 2024 09:56:55 +0100
Subject: [PATCH 2/4] Adding asserts

---
 tools/fastk/fastk.xml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/tools/fastk/fastk.xml b/tools/fastk/fastk.xml
index 407835ac548..6eb6135fdc8 100644
--- a/tools/fastk/fastk.xml
+++ b/tools/fastk/fastk.xml
@@ -63,11 +63,16 @@
         </data>
     </outputs>
     <tests>
-    <!-- TEST 1 -->
+        <!-- TEST 1 -->
         <test expect_num_outputs="2">
             <param name="infile" value="input01.fasta.gz"/>
             <param name="kmer_size" value="40"/>
             <output name="fastk_hist_out" file="test01.hist" ftype="fastk_hist"/>
+            <output name="fastk_out" ftype="tar">
+                <assert_contents>
+                    <has_archive_member path="ktabfiles"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- TEST 2 -->
         <test expect_num_outputs="4">

From c9c0b71d9012117e3a4cede11fdf5b30f887858f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 5 Dec 2024 09:56:02 +0100
Subject: [PATCH 3/4] Update tools/fastk/fastk.xml

---
 tools/fastk/fastk.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/fastk/fastk.xml b/tools/fastk/fastk.xml
index 6eb6135fdc8..bdc08d5d730 100644
--- a/tools/fastk/fastk.xml
+++ b/tools/fastk/fastk.xml
@@ -24,7 +24,7 @@
         -T\${GALAXY_SLOTS:-8} -Noutput -Pktabfiles
         #if $sorted_table.sorted_table_option == 'yes_with_default':
             && Tabex output.ktab -t${sorted_table.tabex_threshold_for_default} LIST > '$tabex_hist'
-            && cp .*.ktab* ktabfiles/ 
+            && cp ".*.ktab*" ktabfiles/ 
             && cp  *.ktab ktabfiles/
         #elif $sorted_table.sorted_table_option == 'yes_with_custom':
             && Tabex output.ktab -t${sorted_table.tabex_threshold_for_custom} LIST > '$tabex_hist'

From 77633d09a2b70ca17c2de7ee11447dc90ca5223f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 5 Dec 2024 15:17:54 +0100
Subject: [PATCH 4/4] Update fastk.xml

---
 tools/fastk/fastk.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/fastk/fastk.xml b/tools/fastk/fastk.xml
index bdc08d5d730..63551cb3efa 100644
--- a/tools/fastk/fastk.xml
+++ b/tools/fastk/fastk.xml
@@ -24,7 +24,7 @@
         -T\${GALAXY_SLOTS:-8} -Noutput -Pktabfiles
         #if $sorted_table.sorted_table_option == 'yes_with_default':
             && Tabex output.ktab -t${sorted_table.tabex_threshold_for_default} LIST > '$tabex_hist'
-            && cp ".*.ktab*" ktabfiles/ 
+            && cp .*.ktab* ktabfiles/ 
             && cp  *.ktab ktabfiles/
         #elif $sorted_table.sorted_table_option == 'yes_with_custom':
             && Tabex output.ktab -t${sorted_table.tabex_threshold_for_custom} LIST > '$tabex_hist'
@@ -119,4 +119,4 @@
 
     ]]></help>
     <expand macro="citations"/>
-</tool>
\ No newline at end of file
+</tool>