annotate macros.xml @ 1:40874f772ea1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit faa8c4bf004428988500537078264968ae05fa67
author iuc
date Mon, 26 Aug 2024 13:47:54 +0000
parents 04d05400d3a6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
1 <macros>
1
40874f772ea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit faa8c4bf004428988500537078264968ae05fa67
iuc
parents: 0
diff changeset
2 <token name="@TOOL_VERSION@">2.3.4</token>
0
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
4 <token name="@PROFILE@">20.09</token>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
5 <token name="@DATATYPES@">fastqsanger.gz,fastqsanger</token>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
6 <xml name="bio_tools">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
7 <xrefs>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
8 <xref type="bio.tools">adapterremoval</xref>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
9 </xrefs>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
10 </xml>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
11 <xml name="requirements">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
12 <requirements>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
13 <requirement type="package" version="@TOOL_VERSION@">adapterremoval</requirement>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
14 </requirements>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
15 </xml>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
16 <xml name="interleaved_output_param">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
17 <param argument="--interleaved_output" type="select" label="Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads?">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
18 <option value="no" selected="true">No</option>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
19 <option value="yes">Yes</option>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
20 </param>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
21 </xml>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
22 <xml name="identify_adapters_param">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
23 <param argument="--identify_adapters" type="boolean" truevalue="--identify-adapters" falsevalue="" checked="false" label="Attempt to build a consensus adapter sequence from fully overlapping pairs of paired-end reads?" help="No trimming is performed in this mode"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
24 </xml>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
25 <xml name="combined_output_param">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
26 <param argument="--combined_output" type="boolean" truevalue="--combined-output" falsevalue="" checked="false" label="Output trimmed reads such that the sequences of reads discarded due to quality filters or read merging are replaced with a single 'N' with Phred score 0?"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
27 </xml>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
28 <xml name="sanitizer">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
29 <sanitizer>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
30 <valid initial="string.printable">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
31 <remove value="&apos;" />
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
32 </valid>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
33 <mapping initial="none">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
34 <add source="&apos;" target="__sq__"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
35 </mapping>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
36 </sanitizer>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
37 </xml>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
38 <xml name="citations">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
39 <citations>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
40 <citation type="doi">10.1186/s13104-016-1900-2</citation>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
41 </citations>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
42 </xml>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
43 </macros>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
44