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changeset 6:6756c87dc2d4 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c"
author iuc
date Thu, 05 Sep 2019 13:14:23 -0400
parents 3905ccd5c631
children
files sickle.xml tool_dependencies.xml
diffstat 2 files changed, 105 insertions(+), 139 deletions(-) [+]
line wrap: on
line diff
--- a/sickle.xml	Thu Apr 13 16:06:10 2017 -0400
+++ b/sickle.xml	Thu Sep 05 13:14:23 2019 -0400
@@ -1,129 +1,126 @@
-<tool id="sickle" name="Sickle" version="1.33.1" profile="17.01">
+<tool id="sickle" name="Sickle" version="1.33.2" profile="17.01">
     <description>windowed adaptive trimming of FASTQ data</description>
     <requirements>
-        <requirement type="package" version="1.33">sickle</requirement>
-        <!-- conda dependency -->
         <requirement type="package" version="1.33">sickle-trim</requirement>
     </requirements>
     <version_command>sickle --version | head -n 1</version_command>
     <command><![CDATA[
-        ## Link in the input files, which also determines the type of the output
-        #set compressed = ""
-        #if str($readtype.single_or_paired) == "se":
-            #if $readtype.input_single.is_of_type('fastq.gz'):
-                #set read1 = "input_1.fastq.gz"
-                #set compressed = "-g"
-            #else
-                #set read1 = "input_1.fastq"
-            #end if
-            ln -f -s '${readtype.input_single}' ${read1} &&
-        #else if str($readtype.single_or_paired) == "pe_combo":
-            #if $readtype.input_combo.is_of_type('fastq.gz'):
-                #set read1 = "input_1.fastq.gz"
-                #set compressed = "-g"
-            #else
-                #set read1 = "input_1.fastq"
-            #end if
-            ln -f -s '${readtype.input_combo}' ${read1} &&
-        #else if str($readtype.single_or_paired) == "pe_sep":
-            #if $readtype.input_paired1.is_of_type('fastq.gz'):
-                #set read1 = "input_1.fastq.gz"
-                #set compressed = "-g"
-            #else
-                #set read1 = "input_1.fastq"
-            #end if
-            ln -f -s '${readtype.input_paired1}' ${read1} &&
+## Link in the input files, which also determines the type of the output
+#set compressed = ""
+#if str($readtype.single_or_paired) == "se":
+    #if $readtype.input_single.is_of_type('fastq.gz'):
+        #set read1 = "input_1.fastq.gz"
+        #set compressed = "-g"
+    #else
+        #set read1 = "input_1.fastq"
+    #end if
+    ln -f -s '${readtype.input_single}' ${read1} &&
+#else if str($readtype.single_or_paired) == "pe_combo":
+    #if $readtype.input_combo.is_of_type('fastq.gz'):
+        #set read1 = "input_1.fastq.gz"
+        #set compressed = "-g"
+    #else
+        #set read1 = "input_1.fastq"
+    #end if
+    ln -f -s '${readtype.input_combo}' ${read1} &&
+#else if str($readtype.single_or_paired) == "pe_sep":
+    #if $readtype.input_paired1.is_of_type('fastq.gz'):
+        #set read1 = "input_1.fastq.gz"
+        #set compressed = "-g"
+    #else
+        #set read1 = "input_1.fastq"
+    #end if
+    ln -f -s '${readtype.input_paired1}' ${read1} &&
 
-            #if $readtype.input_paired2.is_of_type('fastq.gz'):
-                #set read2 = "input_2.fastq.gz"
-            #else
-                #set read2 = "input_2.fastq"
-            #end if
-            ln -f -s '${readtype.input_paired2}' ${read2} &&
-        #else
-            #if $readtype.input_paired.forward.is_of_type('fastq.gz'):
-                #set read1 = "input_1.fastq.gz"
-                #set compressed = "-g"
-            #else
-                #set read1 = "input_1.fastq"
-            #end if
-            ln -f -s '${readtype.input_paired.forward}' ${read1} &&
+    #if $readtype.input_paired2.is_of_type('fastq.gz'):
+        #set read2 = "input_2.fastq.gz"
+    #else
+        #set read2 = "input_2.fastq"
+    #end if
+    ln -f -s '${readtype.input_paired2}' ${read2} &&
+#else
+    #if $readtype.input_paired.forward.is_of_type('fastq.gz'):
+        #set read1 = "input_1.fastq.gz"
+        #set compressed = "-g"
+    #else
+        #set read1 = "input_1.fastq"
+    #end if
+    ln -f -s '${readtype.input_paired.forward}' ${read1} &&
 
-            #if $readtype.input_paired.reverse.is_of_type('fastq.gz'):
-                #set read2 = "input_2.fastq.gz"
-            #else
-                #set read2 = "input_2.fastq"
-            #end if
-            ln -f -s '${readtype.input_paired.reverse}' ${read2} &&
-        #end if
+    #if $readtype.input_paired.reverse.is_of_type('fastq.gz'):
+        #set read2 = "input_2.fastq.gz"
+    #else
+        #set read2 = "input_2.fastq"
+    #end if
+    ln -f -s '${readtype.input_paired.reverse}' ${read2} &&
+#end if
 
-        sickle
+sickle
 
-        #if str($readtype.single_or_paired) == "se":
-            se -f ${read1} -o '${output_single}'
+#if str($readtype.single_or_paired) == "se":
+    se -f ${read1} -o '${output_single}'
 
-            #if $readtype.input_single.is_of_type('fastqillumina', 'fastqillumina.gz'):
-                -t illumina
-            #else if $readtype.input_single.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
-                -t solexa
-            #else:
-                -t sanger
-            #end if
-        #else if str($readtype.single_or_paired) == "pe_combo":
-            #if $readtype.output_n:
-                pe -c ${read1} -M '${output_combo}'
-            #else
-                pe -c ${read1} -m '${output_combo}' -s '${output_combo_single}'
-            #end if
+    #if $readtype.input_single.is_of_type('fastqillumina', 'fastqillumina.gz'):
+        -t illumina
+    #else if $readtype.input_single.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
+        -t solexa
+    #else:
+        -t sanger
+    #end if
+#else if str($readtype.single_or_paired) == "pe_combo":
+    #if $readtype.output_n:
+        pe -c ${read1} -M '${output_combo}'
+    #else
+        pe -c ${read1} -m '${output_combo}' -s '${output_combo_single}'
+    #end if
 
-            #if $readtype.input_combo.is_of_type('fastqillumina', 'fastqillumina.gz'):
-                -t illumina
-            #else if $readtype.input_combo.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
-                -t solexa
-            #else:
-                -t sanger
-            #end if
-        #else if str($readtype.single_or_paired) == "pe_sep":
-            pe -f ${read1} -r ${read2} -o '${output_paired1}' -p '${output_paired2}' -s '${output_paired_single}'
+    #if $readtype.input_combo.is_of_type('fastqillumina', 'fastqillumina.gz'):
+        -t illumina
+    #else if $readtype.input_combo.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
+        -t solexa
+    #else:
+        -t sanger
+    #end if
+#else if str($readtype.single_or_paired) == "pe_sep":
+    pe -f ${read1} -r ${read2} -o '${output_paired1}' -p '${output_paired2}' -s '${output_paired_single}'
 
-            #if $readtype.input_paired1.is_of_type('fastqillumina', 'fastqillumina.gz'):
-                -t illumina
-            #else if $readtype.input_paired1.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
-                -t solexa
-            #else:
-                -t sanger
-            #end if
-        #else if str($readtype.single_or_paired) == "pe_collection":
-            pe -f ${read1} -r ${read2} -o '${output_paired_coll.forward}' -p '${output_paired_coll.reverse}' -s '${output_paired_coll_single}'
+    #if $readtype.input_paired1.is_of_type('fastqillumina', 'fastqillumina.gz'):
+        -t illumina
+    #else if $readtype.input_paired1.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
+        -t solexa
+    #else:
+        -t sanger
+    #end if
+#else if str($readtype.single_or_paired) == "pe_collection":
+    pe -f ${read1} -r ${read2} -o '${output_paired_coll.forward}' -p '${output_paired_coll.reverse}' -s '${output_paired_coll_single}'
 
-            #if $readtype.input_paired.forward.is_of_type('fastqillumina', 'fastqillumina.gz'):
-                -t illumina
-            #else if $readtype.input_paired.forward.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
-                -t solexa
-            #else:
-                -t sanger
-            #end if
-        #end if
+    #if $readtype.input_paired.forward.is_of_type('fastqillumina', 'fastqillumina.gz'):
+        -t illumina
+    #else if $readtype.input_paired.forward.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
+        -t solexa
+    #else:
+        -t sanger
+    #end if
+#end if
 
-        $compressed
+$compressed
 
-        #if str($qual_threshold) != "":
-            -q $qual_threshold
-        #end if
-
-        #if str($length_threshold) != "":
-            -l $length_threshold
-        #end if
+#if str($qual_threshold) != "":
+    -q $qual_threshold
+#end if
 
-        #if $no_five_prime:
-            -x
-        #end if
+#if str($length_threshold) != "":
+    -l $length_threshold
+#end if
 
-        #if $trunc_n:
-            -n
-        #end if
-    ]]>
-    </command>
+#if $no_five_prime:
+    -x
+#end if
+
+#if $trunc_n:
+    -n
+#end if
+    ]]></command>
 
     <inputs>
         <conditional name="readtype">
@@ -350,8 +347,6 @@
 
 Copyright: Nikhil Joshi
 
-http://bioinformatics.ucdavis.edu
-
 http://github.com/najoshi/sickle
     </help>
     <citations>
--- a/tool_dependencies.xml	Thu Apr 13 16:06:10 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="zlib" version="1.2.8">
-        <repository changeset_revision="411985b46ae8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="sickle" version="1.33">
-        <install version="1.0">
-            <actions>
-                <action target_filename="sickle-1.33.tar.gz" type="download_by_url">https://github.com/najoshi/sickle/archive/v1.33.tar.gz</action>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="411985b46ae8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="zlib" version="1.2.8" />
-                    </repository>
-                </action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>sickle</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-Sickle is a windowed adaptive trimming tool for FASTQ files using quality.
-        </readme>
-    </package>
-</tool_dependency>