diff macros.xml @ 16:cd7e644cae1d draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Oct 08 09:57:52 2021 +0000
@@ -0,0 +1,66 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.6.7</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">trim-galore</requirement>
+        </requirements>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">trim_galore</xref>
+        </xrefs>
+    </xml>
+    <xml name="adapter_trimming">
+        <conditional name="trimming">
+            <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">
+                <option value="">Automatic detection</option>
+                <option value="--illumina">Illumina universal</option>
+                <option value="--nextera">Nextera transposase</option>
+                <option value="--small_rna">Illumina small RNA adapters</option>
+                <option value="user">User defined adapter sequence</option>
+            </param>
+            <when value=""/>
+            <when value="--illumina"/>
+            <when value="--nextera"/>
+            <when value="--small_rna"/>
+            <when value="user">
+                <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">
+                    <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
+                </param>
+                <yield/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="paired_adapter_trimming">
+        <expand macro="adapter_trimming">
+            <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
+                <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
+            </param>
+        </expand>
+        <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" />
+        <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
+            <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
+                This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
+                (--three_prime_clip_R1)</help>
+        </param>
+        <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 2">
+            <help>Instructs Trim Galore! to remove N bp from the 3' end of read 2 after
+                adapter/quality trimming has been performed. This may remove some unwanted bias from
+                the 3' end that is not directly related to adapter sequence or basecall quality.</help>
+        </param>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{githubTrim_Galore,
+                author = {Krueger, Felix},
+                year = {2021},
+                title = {Trim Galore},
+                publisher = {GitHub},
+                journal = {GitHub repository},
+                url = {https://https://github.com/FelixKrueger/TrimGalore.com/fenderglass/Flye}}
+            </citation>        
+        </citations>
+    </xml>
+</macros>