diff hisat2_macros.xml @ 0:5bafe7d7a55e draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hisat2_macros.xml	Sat Oct 10 14:54:39 2015 -0400
@@ -0,0 +1,66 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="function" tokens="helptext">
+        <param display="radio" help="@HELPTEXT@" label="Function type" name="function_type" type="select">
+            <option value="C">Constant</option>
+            <option value="L">Linear [f(x) = y + z * x]</option>
+            <option value="S">Square root [f(x) = y + z * x&#178;]</option>
+            <option value="G">Natural logarithm [f(x) = y + z * log(x)]</option>
+        </param>
+        <param help="@HELPTEXT@" label="Constant term (y)" name="constant_term" type="integer" value="0" />
+        <param help="@HELPTEXT@" label="Coefficient (z)" name="coefficient" type="integer" value="0" />
+    </xml>
+    <xml name="single_paired_selector">
+        <param label="Single end or paired reads?" name="paired_selector" type="select">
+            <option value="paired_collection">Collection of paired reads</option>
+            <option value="paired">Individual paired reads</option>
+            <option value="single">Individual unpaired reads</option>
+        </param>
+    </xml>
+    <xml name="paired_input_conditional" tokens="ftype">
+        <conditional name="paired">
+            <expand macro="single_paired_selector" />
+            <when value="paired_collection">
+                <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" />
+                <expand macro="paired_end_conditional" />
+            </when>
+            <when value="paired">
+                <param format="@FTYPE@" label="Forward reads" multiple="true" name="reads_f" type="data" />
+                <param format="@FTYPE@" label="Reverse reads" multiple="true" name="reads_r" type="data" />
+                <expand macro="paired_end_conditional" />
+            </when>
+            <when value="single">
+                <param format="@FTYPE@" label="Reads" multiple="true" name="reads" type="data" />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="paired_end_conditional">
+        <conditional name="paired_end_options">
+            <param label="Paired-end options" name="paired_end_options_selector" type="select">
+                <option value="defaults">Use default values</option>
+                <option value="advanced">Specify paired-end parameters</option>
+            </param>
+            <when value="defaults" />
+            <when value="advanced">
+                <param name="no_mixed" label="Disable alignments of individual mates" type="boolean" truevalue="--no-mixed" falsevalue=""
+                    help="By default, when hisat cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior. (--no-mixed)" />
+                <param name="no_discordant" label="Disable discordant alignments" type="boolean" truevalue="--no-discordant" falsevalue=""
+                    help="By default, hisat looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior. (--no-discordant)" />
+                <param name="skip_reverse" label="Skip reference strand of reference" type="boolean" truevalue="--norc" falsevalue="" help="(--norc) If --norc is specified, hisat will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand." />
+            </when>
+        </conditional>
+    </xml>
+    <token name="@paired_end_options@">
+        #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced':
+            ${input_format.paired.paired_end_options.no_mixed}
+            ${input_format.paired.paired_end_options.no_discordant}
+        #end if
+    </token>
+    <token name="strandedness_parameters">
+        #if str($spliced_options.spliced_options_selector) == "advanced":
+            #if str($spliced_options.rna_strandness).strip() != '':
+                --rna-strandness $spliced_options.rna_strandness
+            #end if
+        #end if
+    </token>
+</macros>