diff logex.xml @ 0:73ddd200456a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/logex.xml	Tue Jan 07 13:40:30 2025 +0000
@@ -0,0 +1,92 @@
+<tool id="fastk_logex" name="FastK Logex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="MIT">
+    <description>Performs binary operations on the generated Ktab files from FASTK suite</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p logex_ktabs
+        && mkdir -p input_files
+        && cp '$input_ktab1' input_files/input1.ktab
+        && ln -s '$input_ktab1_tar' input1.tar
+        && tar -xf input1.tar 
+        && mv ktabfiles ktabfiles_in1
+        && mv "\$(find ktabfiles_in1 -type f -name '*.ktab.1')" "ktabfiles_in1/.input1.ktab.1"
+        && cp '$input_ktab2' input_files/input2.ktab
+        && ln -s '$input_ktab2_tar' input2.tar
+        && tar -xf input2.tar
+        && mv ktabfiles ktabfiles_in2
+        && mv "\$(find ktabfiles_in2 -type f -name '*.ktab.1')" "ktabfiles_in2/.input2.ktab.1"
+        && mv ktabfiles_in1/.input1.ktab.1 input_files/
+        && mv ktabfiles_in2/.input2.ktab.1 input_files/ &&
+        #if $operation_selector == 'and':
+            Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&.B' input_files/input1.ktab input_files/input2.ktab
+        #elif $operation_selector == 'or':
+            Logex -T\${GALAXY_SLOTS:-8} -h 'out = A|.B' input_files/input1.ktab input_files/input2.ktab
+        #elif $operation_selector == 'minus':
+            Logex -T\${GALAXY_SLOTS:-8} -h 'out = A-B' input_files/input1.ktab input_files/input2.ktab
+        #elif $operation_selector == 'xor':
+            Logex -T\${GALAXY_SLOTS:-8} -h 'out = A^B' input_files/input1.ktab input_files/input2.ktab
+        #elif $operation_selector == 'unionsum':
+            Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&+B' input_files/input1.ktab input_files/input2.ktab
+        #end if
+        && cp *.ktab logex_ktabs/
+        && cp .*.ktab* logex_ktabs/
+        && tar -cf logex_ktab.tar input_files/ logex_ktabs/
+    ]]></command>
+    <inputs>
+        <param name="input_ktab1" type="data" format="fastk_ktab" label="Input FastK ktab file (first)"/>
+        <param name="input_ktab1_tar" type="data" format="fastk_ktab" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
+        <param name="input_ktab2" type="data" format="fastk_ktab" label="Input FastK ktab file (second)"/>
+        <param name="input_ktab2_tar" type="data" format="fastk_ktab" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
+        <param name="operation_selector" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files.">
+            <option value="and">AND</option>
+            <option value="or">OR</option>
+            <option value="minus">Minus</option>
+            <option value="unionsum">Unionsum</option>
+            <option value="xor">XOR</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="fastk_hist_out" format="fastk_hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Logex .hist file"/>
+        <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="out.ktab" label="${tool.name} on ${on_string}: Logex .ktab file"/>
+        <data name="fastk_ktab_files" format="tar" from_work_dir="logex_ktab.tar" label="${tool.name} on ${on_string}: FastK Logex ktab files"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="3">
+            <param name="input_ktab1" value="fastq1.ktab"/>
+            <param name="input_ktab1_tar" value="fastk_in1.tar"/>
+            <param name="input_ktab2" value="fastq2.ktab"/>
+            <param name="input_ktab2_tar" value="fastk_in2.tar"/>
+            <param name="operation_selector" value="AND"/>
+            <output name="fastk_hist_out" ftype="fastk_hist">
+                <assert_contents>
+                    <has_size value="262164"/>
+                </assert_contents>
+            </output>
+            <output name="fastk_ktab_out" ftype="fastk_ktab">
+                <assert_contents>
+                    <has_size value="2064"/>
+                </assert_contents>
+            </output>
+            <output name="fastk_ktab_files" ftype="tar">
+                <assert_contents>
+                    <has_archive_member path="logex_ktabs/out.ktab"/>
+                    <has_archive_member path="logex_ktabs/.out.ktab.1"/>
+                    <has_archive_member path="input_files/input1.ktab"/>
+                    <has_archive_member path="input_files/.input1.ktab.1"/>
+                    <has_archive_member path="input_files/input2.ktab"/>
+                    <has_archive_member path="input_files/.input2.ktab.1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+     Logex tool can perform operations such as AND, OR, XOR, Minus and Unionsum on the input given input Ktab files.
+     
+     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.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file