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

Changeset 3:9b1aebbaec34 (2025-05-10)
Previous changeset 2:ec82f2b95e89 (2025-02-19) Next changeset 4:94217ea28453 (2025-05-14)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
modified:
logex.xml
b
diff -r ec82f2b95e89 -r 9b1aebbaec34 logex.xml
--- a/logex.xml Wed Feb 19 11:17:07 2025 +0000
+++ b/logex.xml Sat May 10 09:09:02 2025 +0000
[
b'@@ -1,4 +1,4 @@\n-<tool id="fastk_logex" name="FastK Logex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT">\n+<tool id="fastk_logex" name="FastK Logex" version="@TOOL_VERSION@+galaxy3" profile="24.2" license="MIT">\n     <description>Performs binary operations on the generated Ktab files from FASTK suite</description>\n     <macros>\n         <import>macros.xml</import>\n@@ -6,47 +6,119 @@\n     <expand macro="xrefs"/>\n     <expand macro="requirements"/>\n     <command detect_errors="exit_code"><![CDATA[\n-        mkdir -p logex_ktabs\n-        && mkdir -p input_files\n-        && cp \'$input_ktab1\' input_files/input1.ktab\n-        && ln -s \'$input_ktab1_tar\' input1.tar\n-        && tar -xf input1.tar \n-        && mv ktabfiles ktabfiles_in1\n-        && mv "\\$(find ktabfiles_in1 -type f -name \'*.ktab.1\')" "ktabfiles_in1/.input1.ktab.1"\n-        && cp \'$input_ktab2\' input_files/input2.ktab\n-        && ln -s \'$input_ktab2_tar\' input2.tar\n-        && tar -xf input2.tar\n-        && mv ktabfiles ktabfiles_in2\n-        && mv "\\$(find ktabfiles_in2 -type f -name \'*.ktab.1\')" "ktabfiles_in2/.input2.ktab.1"\n-        && mv ktabfiles_in1/.input1.ktab.1 input_files/\n-        && mv ktabfiles_in2/.input2.ktab.1 input_files/ &&\n-        #if $operation_selector == \'and\':\n-            Logex -T\\${GALAXY_SLOTS:-8} -h \'out = A&.B\' input_files/input1.ktab input_files/input2.ktab\n-        #elif $operation_selector == \'or\':\n-            Logex -T\\${GALAXY_SLOTS:-8} -h \'out = A|.B\' input_files/input1.ktab input_files/input2.ktab\n-        #elif $operation_selector == \'minus\':\n-            Logex -T\\${GALAXY_SLOTS:-8} -h \'out = A-B\' input_files/input1.ktab input_files/input2.ktab\n-        #elif $operation_selector == \'xor\':\n-            Logex -T\\${GALAXY_SLOTS:-8} -h \'out = A^B\' input_files/input1.ktab input_files/input2.ktab\n-        #elif $operation_selector == \'unionsum\':\n-            Logex -T\\${GALAXY_SLOTS:-8} -h \'out = A&+B\' input_files/input1.ktab input_files/input2.ktab\n+        mkdir -p logex_ktabs &&\n+        mkdir -p input_files &&\n+        #if $input_type.input_type_selector != \'collection\'\n+            cp \'$input_ktab1\' input_files/input1.ktab &&\n+            ln -s \'$input_ktab1_tar\' input1.tar &&\n+            tar -xf input1.tar && \n+            mv ktabfiles ktabfiles_in1 &&\n+            mv "\\$(find ktabfiles_in1 -type f -name \'*.ktab.1\')" "ktabfiles_in1/.input1.ktab.1" &&\n+            cp \'$input_ktab2\' input_files/input2.ktab &&\n+            ln -s \'$input_ktab2_tar\' input2.tar &&\n+            tar -xf input2.tar &&\n+            mv ktabfiles ktabfiles_in2 &&\n+            mv "\\$(find ktabfiles_in2 -type f -name \'*.ktab.1\')" "ktabfiles_in2/.input2.ktab.1" &&\n+            mv ktabfiles_in1/.input1.ktab.1 input_files/ &&\n+            mv ktabfiles_in2/.input2.ktab.1 input_files/ &&\n+            #if $input_type.operation_selector == \'and\'\n+                Logex -T\\${GALAXY_SLOTS:-8} -h \'out = A&.B\' input_files/input1.ktab input_files/input2.ktab &&\n+            #elif $input_type.operation_selector == \'or\'\n+                Logex -T\\${GALAXY_SLOTS:-8} -h \'out = A|.B\' input_files/input1.ktab input_files/input2.ktab &&\n+            #elif $input_type.operation_selector == \'minus\'\n+                Logex -T\\${GALAXY_SLOTS:-8} -h \'out = A-B\' input_files/input1.ktab input_files/input2.ktab &&\n+            #elif $input_type.operation_selector == \'xor\'\n+                Logex -T\\${GALAXY_SLOTS:-8} -h \'out = A^B\' input_files/input1.ktab input_files/input2.ktab && \n+            #elif $input_type.operation_selector == \'unionsum\'\n+                Logex -T\\${GALAXY_SLOTS:-8} -h \'out = A&+B\' input_files/input1.ktab input_files/input2.ktab &&\n+            #end if\n+        #else\n+            #for $i, $j in enumerate($input_type.input_ktab_collection):\n+                cp "$j" input_files/${i+1}.ktab &&\n+            #end for\n+            #for $p, $q in enumerate($input_type.input_ktab_collection_tar):\n+                ln -s "$q" input_files/input_ktab_$'..b'">\n+                        <element name="input1" value="fastk_in1.tar"/>\n+                        <element name="input2" value="fastk_in2.tar"/>\n+                    </collection>\n+                </param>\n+                <conditional name="operation_sel">\n+                    <param name="operation_selector_collection" value="unionsum"/>\n+                </conditional>\n+            </conditional>\n+            <output name="fastk_hist_out" ftype="fastk_hist">\n+                <assert_contents>\n+                    <has_size value="262164"/>\n+                </assert_contents>\n+            </output>\n+            <output name="fastk_ktab_out" ftype="fastk_ktab">\n+                <assert_contents>\n+                    <has_size value="2064"/>\n+                </assert_contents>\n+            </output>\n+            <output name="fastk_ktab_files" ftype="fastk_ktab_tar">\n+                <assert_contents>\n+                    <has_archive_member path="logex_ktabs/out.ktab"/>\n+                    <has_archive_member path="logex_ktabs/.out.ktab.1"/>\n+                    <has_archive_member path="input_files/1.ktab"/>\n+                    <has_archive_member path="input_files/.1.ktab.1"/>\n+                    <has_archive_member path="input_files/2.ktab"/>\n+                    <has_archive_member path="input_files/.2.ktab.1"/>\n+                </assert_contents>\n+            </output>\n+        </test>\n+        <test expect_num_outputs="3">\n+            <conditional name="input_type">\n+                <param name="input_type_selector" value="collection"/>\n+                <param name="input_ktab_collection">\n+                    <collection type="list">\n+                        <element name="input1" value="fastq1.ktab"/>\n+                        <element name="input2" value="fastq2.ktab"/>\n+                    </collection>\n+                </param>\n+                <param name="input_ktab_collection_tar">\n+                    <collection type="list">\n+                        <element name="input1" value="fastk_in1.tar"/>\n+                        <element name="input2" value="fastk_in2.tar"/>\n+                    </collection>\n+                </param>\n+                <conditional name="operation_sel">\n+                    <param name="operation_selector_collection" value="custom"/>\n+                    <param name="custom_expression" value="A&amp;.B"/>\n+                </conditional>\n+            </conditional>\n+            <output name="fastk_hist_out" ftype="fastk_hist">\n+                <assert_contents>\n+                    <has_size value="262164"/>\n+                </assert_contents>\n+            </output>\n+            <output name="fastk_ktab_out" ftype="fastk_ktab">\n+                <assert_contents>\n+                    <has_size value="2064"/>\n+                </assert_contents>\n+            </output>\n+            <output name="fastk_ktab_files" ftype="fastk_ktab_tar">\n+                <assert_contents>\n+                    <has_archive_member path="logex_ktabs/out.ktab"/>\n+                    <has_archive_member path="logex_ktabs/.out.ktab.1"/>\n+                    <has_archive_member path="input_files/1.ktab"/>\n+                    <has_archive_member path="input_files/.1.ktab.1"/>\n+                    <has_archive_member path="input_files/2.ktab"/>\n+                    <has_archive_member path="input_files/.2.ktab.1"/>\n+                </assert_contents>\n+            </output>\n+        </test>\n     </tests>\n     <help><![CDATA[\n \n      Logex tool can perform operations such as AND, OR, XOR, Minus and Unionsum on the input given input Ktab files.\n      \n      The tool requires two input Ktab files and their associated files (Generated in the tarball of FASTK tool with .1 extension) as inputs to perform various binary operations.\n+    \n+    The tool also supports Ktab file collections as input. The user can select the operation to be performed on the input Ktab files.\n \n     ]]></help>\n     <expand macro="citations"/>\n'