diff rseqc_macros.xml @ 3:71ed55a3515a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rseqc_macros.xml	Tue Mar 14 10:22:57 2017 -0400
@@ -0,0 +1,155 @@
+<macros>
+
+    <token name="@WRAPPER_VERSION@">2.6.4</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.6.4">rseqc</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
+            <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
+        </stdio>
+    </xml>
+
+    <!-- Params -->
+    <xml name="bam_param">
+        <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/>
+    </xml>
+
+    <xml name="bam_sam_param">
+        <param name="input" type="data" label="Input .bam/.sam file" format="bam,sam" help="(--input-file)"/>
+    </xml>
+
+    <xml name="refgene_param">
+        <param name="refgene" type="data" format="bed" label="Reference gene model" help="(--refgene)"/>
+    </xml>
+
+    <xml name="mapq_param">
+        <param name="mapq" type="integer" label="Minimum mapping quality" value="30" help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot; (--mapq)"/>
+    </xml>
+
+    <xml name="readlength_param">
+        <param name="readlength" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length (--read-align-length)"/>
+    </xml>
+
+    <xml name="readnum_param">
+        <param name="readnum" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile (--read-num)"/>
+    </xml>
+
+    <xml name="sample_size_param">
+        <param name="sample_size" type="integer" label="Number of reads sampled from SAM/BAM file (default = 200000)" value="200000" min="1" help="(--sample-size)"/>
+    </xml>
+
+    <xml name="min_intron_param">
+        <param name="min_intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" help="(--min-intron)" />
+    </xml>
+
+    <xml name="layout_param">
+        <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)">
+            <option value="SE" selected="true">Single-end</option>
+            <option value="PE">Paired-end</option>
+        </param>
+    </xml>
+
+    <xml name="strand_type_param">
+        <conditional name="strand_type">
+            <param name="strand_specific" type="select" label="Strand-specific?">
+                <option value="none" selected="true">None</option>
+                <option value="pair">Pair-End RNA-seq</option>
+                <option value="single">Single-End RNA-seq</option>
+            </param>
+            <when value="pair">
+                <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" help="(--strand)">
+                    <option value="sd" selected="true"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
+                    <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
+                </param>
+            </when>
+            <when value="single">
+                <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" help="(--strand)">
+                    <option value="s" selected="true">positive --> positive; negative --> negative</option>
+                    <option value="d">positive --> negative; negative --> positive</option>
+                </param>
+            </when>
+            <when value="none"></when>
+        </conditional>
+    </xml>
+
+    <xml name="multihits_param">
+        <conditional name="multihits_type">
+            <param name="multihits_type_selector" type="select" label="Reads with multiple hits" help="(--skip-multi-hits)">
+                <option value="use_multihits" selected="true">Count Mutliple Hit Reads</option>
+                <option value="skip_multihits">Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads</option>
+            </param>
+            <when value="skip_multihits">
+                <expand macro="mapq_param" />
+            </when>
+            <when value="use_multihits" />
+        </conditional>
+    </xml>
+
+    <xml name="rscript_output_param">
+        <param name="rscript_output" type="boolean" value="false" label="Output R-Script"
+            help="Output the R-Script used to generate the plots" />
+    </xml>
+
+
+    <!-- Output -->
+
+    <xml name="pdf_output_data" token_filename="output.pdf">
+        <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (pdf)" />
+    </xml>
+
+    <xml name="xls_output_data" token_filename="output.xls">
+        <data format="xls" name="outputxls" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (xls)" />
+    </xml>
+
+    <xml name="rscript_output_data" token_filename="output.r">
+        <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (rscript)">
+            <filter>rscript_output</filter>
+        </data>
+    </xml>
+
+    <!-- Command -->
+    <token name="@MULTIHITS@">
+<![CDATA[
+#if str($multihits_type.multihits_type_selector) == "skip_multihits"
+    --skip-multi-hits
+    --mapq=${multihits_type.mapq}
+#end if
+]]>
+    </token>
+
+    <token name="@ABOUT@">
+
+-----
+
+About RSeQC
++++++++++++
+
+The RSeQC_ package provides a number of useful modules that can comprehensively
+evaluate high throughput sequence data especially RNA-seq data. "Basic modules"
+quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC
+bias, while "RNA-seq specific modules" investigate sequencing saturation status
+of both splicing junction detection and expression estimation, mapped reads
+clipping profile, mapped reads distribution, coverage uniformity over gene
+body, reproducibility, strand specificity and splice junction annotation.
+
+The RSeQC package is licensed under the GNU GPL v3 license.
+
+.. image:: $PATH_TO_IMAGES/logo.png
+
+.. _RSeQC: http://rseqc.sourceforge.net/
+
+
+    </token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/bts356</citation>
+        </citations>
+    </xml>
+</macros>