Mercurial > repos > iuc > multiqc

diff star_plugin.xml @ 24:f7e2f1eb3a16 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
author: iuc
date: Mon, 02 Sep 2024 14:22:54 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/star_plugin.xml	Mon Sep 02 14:22:54 2024 +0000
@@ -0,0 +1,77 @@
+<macros>
+    <token name="@STAR_COMMAND@"><![CDATA[
+        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+            @CREATE_REPEAT_DIR_2@
+            #if str($repeat2.type.type) == "log"
+                #for $file in $repeat2.type.input
+                    @ESCAPE_IDENTIFIER@
+                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out')
+                    ln -s '$file' '$file_path' &&
+                #end for
+            #elif str($repeat2.type.type) == "genecounts"
+                #for $file in $repeat2.type.input
+                    @ESCAPE_IDENTIFIER@
+                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab')
+                    ln -s '$file' '$file_path' &&
+                #end for
+            #end if
+        #end for
+    ]]></token>
+    <xml name="star_form">
+        <repeat name="output" title="STAR output" min="1">
+            <conditional name="type">
+                <param name="type" type="select" label="Type of STAR output?">
+                    <option value="log">Log</option>
+                    <option value="genecounts">Gene counts</option>
+                </param>
+                <when value="log">
+                    <param name="input" type="data" format="txt" label="STAR log output" multiple="true"/>
+                </when>
+                <when value="genecounts">
+                    <param name="input" type="data" format="tabular,tsv" label="STAR gene count output" multiple="true"/>
+                </when>
+            </conditional>
+        </repeat>
+    </xml>
+    <xml name="star_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="star"/>
+                    <repeat name="output">
+                        <conditional name="type">
+                            <param name="type" value="log"/>
+                            <param name="input" value="star_log.txt"/>
+                        </conditional>
+                    </repeat>
+                    <repeat name="output">
+                        <conditional name="type">
+                            <param name="type" value="genecounts"/>
+                            <param name="input" value="star_counts.txt"/>
+                        </conditional>
+                    </repeat>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="star_alignment_plot"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="STAR_mqc_generalstats_star_uniquely_mapped_percent"/>
+                    <has_text text="star_log_txt"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="7"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="1"/>
+        </test>
+    </xml>
+</macros>