annotate catWrapper.xml @ 8:5b2cc63d7a21 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
author artbio
date Fri, 13 Oct 2023 09:46:58 +0000
parents 55cf9d9defd1
children 5b1b635232ed
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
1 <tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.2">
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
2 <description>tail-to-head while specifying how</description>
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
3 <command><![CDATA[
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
4 #if $headers == 0:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
5 #set $concat_command = "cat"
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
6 #else:
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
7 #set $concat_command = 'tail -q -n +'+ str(int($headers)+1)
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
8 #end if
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
9 printf "Concatenating files:\n" &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
10 #if $global_condition.input_type == "singles":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
11 #if $dataset_names == "No":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
12 #for $file in $global_condition.inputs
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
13 printf "${file.element_identifier}..." &&
7
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
14 #if $file.ext:
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
15 #if $file.ext[-2:] == "gz" and $headers != 0:
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
16 gzip -dc '$file' | $concat_command | gzip -c >> '$out_file1' &&
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
17 #else:
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
18 $concat_command '$file' >> '$out_file1' &&
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
19 #end if
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
20 #else:
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
21 $concat_command '$file' >> '$out_file1' &&
7
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
22 #end if
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
23 printf "Done\n" &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
24 #end for
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
25 sleep 1
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
26 #else:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
27 #for $file in $global_condition.inputs
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
28 printf "${file.element_identifier}..." &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
29 #if $file.ext[-2:] == "gz" and $headers != 0:
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
30 printf "# ${file.element_identifier}\n" | gzip -c >> '$out_file1' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
31 gzip -dc "$file" | $concat_command |gzip -c >> '$out_file1' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
32 #else:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
33 printf "# ${file.element_identifier}\n" >> '$out_file1' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
34 $concat_command "$file" >> '$out_file1' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
35 #end if
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
36 printf "Done\n" &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
37 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
38 sleep 1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
39 #end if
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
40 #else if $global_condition.input_type == "simple_collections":
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
41 mkdir concatenated &&
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
42 #if $dataset_names == "No":
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
43 #for $x, $y in zip($global_condition.input_1, $global_condition.input_2):
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
44 printf "${x.element_identifier} and ${y.element_identifier}..." &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
45 #if $x.ext[-2:] == "gz" and $headers != 0:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
46 gzip -dc '$x' | $concat_command | gzip -c > concatenated/'${x.element_identifier}.listed.${x.ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
47 gzip -dc '$y' | $concat_command | gzip -c >> concatenated/'${x.element_identifier}.listed.${x.ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
48 #else:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
49 $concat_command '$x' '$y' > concatenated/'${x.element_identifier}.listed.${x.ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
50 #end if
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
51 printf "Done\n" &&
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
52 #end for
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
53 sleep 1
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
54 #else:
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
55 #for $x, $y in zip($global_condition.input_1, $global_condition.input_2)
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
56 printf "${x.element_identifier} and ${y.element_identifier}..." &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
57 #if $x.ext[-2:] == "gz" and $headers != 0:
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
58 printf "# ${x.element_identifier}\n" | gzip -c > concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' &&
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
59 gzip -dc '$x' | $concat_command | gzip -c >> concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' &&
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
60 printf "# ${y.element_identifier}\n" | gzip -c >> concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' &&
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
61 gzip -dc '$y' | $concat_command | gzip -c >> concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' &&
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
62 #else:
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
63 printf "# ${x.element_identifier}\n" > concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' &&
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
64 $concat_command '$x'>> concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' &&
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
65 printf "# ${y.element_identifier}\n" >> concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' &&
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
66 $concat_command '$y' >> concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' &&
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
67 #end if
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
68 printf "Done\n" &&
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
69 #end for
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
70 sleep 1
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
71 #end if
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
72 #else if $global_condition.input_type == "paired_collection":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
73 #if $global_condition.paired_cat_type == "by_strand":
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
74 mkdir concatenated &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
75 #if $dataset_names == "No":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
76 #for $file in $global_condition.inputs
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
77 printf "${file.element_identifier}- forward and reverse..." &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
78 #if $file['forward'].ext[-2:] == "gz" and $headers != 0:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
79 gzip -dc $file['forward'] | $concat_command | gzip -c >> concatenated/forward.listed.${file['forward'].ext}.listed &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
80 gzip -dc $file['reverse'] | $concat_command | gzip -c >> concatenated/reverse.listed.${file['reverse'].ext}.listed &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
81 #else:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
82 $concat_command $file['forward'] >> concatenated/forward.listed.${file['forward'].ext}.listed &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
83 $concat_command $file['reverse'] >> concatenated/reverse.listed.${file['reverse'].ext}.listed &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
84 #end if
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
85 printf "Done\n" &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
86 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
87 sleep 1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
88 #else:
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
89 #for $file in $global_condition.inputs.keys():
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
90 printf "$file - forward and reverse..." &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
91 #if $global_condition.inputs[$file]['forward'].ext[-2:] == "gz" and $headers != 0:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
92 printf "# ${file}_forward\n" | gzip -c >> concatenated/forward.listed.${global_condition.inputs[$file]['forward'].ext}.listed &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
93 gzip -dc $global_condition.inputs[$file]['forward'] | $concat_command | gzip -c >> concatenated/forward.listed.${global_condition.inputs[$file]['forward'].ext}.listed &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
94 printf "# ${file}_reverse\n" | gzip -c >> concatenated/reverse.listed.${global_condition.inputs[$file]['reverse'].ext}.listed &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
95 gzip -dc $global_condition.inputs[$file]['reverse'] | $concat_command | gzip -c >> concatenated/reverse.listed.${global_condition.inputs[$file]['reverse'].ext}.listed &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
96 #else:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
97 printf "# ${file}_forward\n" >> concatenated/forward.listed.${global_condition.inputs[$file]['forward'].ext}.listed &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
98 $concat_command $global_condition.inputs[$file]['forward'] >> concatenated/forward.listed.${global_condition.inputs[$file]['forward'].ext}.listed &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
99 printf "# ${file}_reverse\n" >> concatenated/reverse.listed.${global_condition.inputs[$file]['reverse'].ext}.listed &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
100 $concat_command $global_condition.inputs[$file]['reverse'] >> concatenated/reverse.listed.${global_condition.inputs[$file]['reverse'].ext}.listed &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
101 #end if
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
102 printf "Done\n" &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
103 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
104 sleep 1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
105 #end if
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
106 #else if $global_condition.paired_cat_type == "by_pair":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
107 mkdir concatenated &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
108 #if $dataset_names == "No":
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
109 #for $file in $global_condition.inputs.keys():
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
110 printf "$file - forward and reverse..." &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
111 #if $global_condition.inputs[$file]['forward'].ext[-2:] == "gz" and $headers != 0:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
112 gzip -dc $global_condition.inputs[$file]['forward'] | $concat_command | gzip -c
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
113 > concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
114 gzip -dc $global_condition.inputs[$file]['reverse'] | $concat_command | gzip -c
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
115 >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
116 #else:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
117 $concat_command $global_condition.inputs[$file]['forward']
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
118 > concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
119 $concat_command $global_condition.inputs[$file]['reverse']
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
120 >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
121 #end if
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
122 printf "Done\n" &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
123 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
124 sleep 1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
125 #else:
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
126 #for $file in $global_condition.inputs.keys():
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
127 printf "$file - forward and reverse..." &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
128 #if $global_condition.inputs[$file]['reverse'].ext[-2:] == "gz" and $headers != 0:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
129 printf "# ${file}_forward\n" | gzip -c > concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
130 gzip -dc $global_condition.inputs[$file]['forward'] | $concat_command | gzip -c
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
131 >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
132 printf "# ${file}_reverse\n" | gzip -c >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
133 gzip -dc $global_condition.inputs[$file]['reverse'] | $concat_command | gzip -c
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
134 >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
135 #else:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
136 printf "# ${file}_forward\n" > concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
137 $concat_command $global_condition.inputs[$file]['forward']
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
138 >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
139 printf "# ${file}_reverse\n" >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
140 $concat_command $global_condition.inputs[$file]['reverse']
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
141 >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
142 #end if
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
143 printf "Done\n" &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
144 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
145 sleep 1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
146 #end if
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
147 #else if $global_condition.paired_cat_type == "all":
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
148 mkdir concatenated &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
149 #set $base_name=$global_condition.inputs.element_identifier
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
150 #set $extention=$global_condition.inputs[$global_condition.inputs.keys()[0]]['forward'].ext
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
151 #if $dataset_names == "No":
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
152 #for $file in $global_condition.inputs.keys():
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
153 printf "$file - forward and reverse..." &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
154 #if $global_condition.inputs[$file]['forward'].ext[-2:] == "gz" and $headers != 0:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
155 gzip -dc $global_condition.inputs[$file]['forward'] | $concat_command | gzip -c >> c'$paired_out_file' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
156 gzip -dc $global_condition.inputs[$file]['reverse'] | $concat_command | gzip -c >> '$paired_out_file' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
157 #else:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
158 $concat_command
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
159 $global_condition.inputs[$file]['forward']
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
160 >> '$paired_out_file' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
161 $concat_command
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
162 $global_condition.inputs[$file]['reverse']
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
163 >> '$paired_out_file' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
164 #end if
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
165 printf "Done\n" &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
166 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
167 sleep 1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
168 #else:
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
169 #for $file in $global_condition.inputs.keys():
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
170 printf "$file - forward and reverse..." &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
171 #if $global_condition.inputs[$file]['forward'].ext[-2:] == "gz" and $headers != 0:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
172 printf "# ${file}_forward\n" | gzip -c > '$paired_out_file' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
173 gzip -dc $global_condition.inputs[$file]['forward'] | $concat_command | gzip -c >> '$paired_out_file' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
174 printf "# ${file}_reverse\n" | gzip -c >> '$paired_out_file' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
175 gzip -dc $global_condition.inputs[$file]['reverse'] | $concat_command | gzip -c >> '$paired_out_file' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
176 #else:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
177 printf "# ${file}_forward\n" > '$paired_out_file' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
178 $concat_command
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
179 $global_condition.inputs[$file]['forward']
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
180 >> '$paired_out_file' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
181 printf "# ${file}_reverse\n" >> '$paired_out_file' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
182 $concat_command
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
183 $global_condition.inputs[$file]['reverse']
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
184 >> '$paired_out_file' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
185 #end if
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
186 printf "Done\n" &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
187 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
188 sleep 1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
189 #end if
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
190 #end if
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
191 #else if $global_condition.input_type == "nested_collection":
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
192 mkdir concatenated &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
193 #if $dataset_names == "No":
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
194 #for $sub_list in $global_condition.inputs:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
195 #set $file_base_name=$sub_list.element_identifier
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
196 #for $sub_list_element in $sub_list:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
197 printf "${file_base_name} - ${sub_list_element.element_identifier}..." &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
198 #if $sub_list_element.ext[-2:] == "gz" and $headers != 0:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
199 gzip -dc ${sub_list_element} | $concat_command | gzip -c >> concatenated/'${file_base_name}.listed.${sub_list_element.ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
200 #else:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
201 $concat_command ${sub_list_element} >> concatenated/'${file_base_name}.listed.${sub_list_element.ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
202 #end if
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
203 printf "Done\n" &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
204 #end for
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
205 #end for
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
206 sleep 1
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
207 #else:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
208 #for $sub_list in $global_condition.inputs:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
209 #set $file_base_name=$sub_list.element_identifier
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
210 #for $sub_list_element in $sub_list:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
211 printf "${file_base_name} - ${sub_list_element.element_identifier}..." &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
212 #if $sub_list_element.ext[-2:] == "gz" and $headers != 0:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
213 printf "# ${sub_list_element.element_identifier}\n" | gzip -c >> concatenated/'${file_base_name}.listed.${sub_list_element.ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
214 gzip -dc ${sub_list_element} | $concat_command | gzip -c >> concatenated/'${file_base_name}.listed.${sub_list_element.ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
215 #else:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
216 printf "# ${sub_list_element.element_identifier}\n" >> concatenated/'${file_base_name}.listed.${sub_list_element.ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
217 $concat_command ${sub_list_element} >> concatenated/'${file_base_name}.listed.${sub_list_element.ext}.listed' &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
218 #end if
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
219 printf "Done\n" &&
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
220 #end for
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
221 #end for
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
222 sleep 1
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
223 #end if
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
224 #end if
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
225 ]]>
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
226 </command>
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
227 <inputs>
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
228 <conditional name="global_condition">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
229 <param name="input_type" type="select" label="What type of data do you wish to concatenate?" help="Depending on the type of input selected the concatenation options will differ">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
230 <option value="singles">Single datasets</option>
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
231 <option value="simple_collections">2 Collections</option>
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
232 <option value="paired_collection">Paired collection</option>
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
233 <option value="nested_collection">Nested collection</option>
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
234 </param>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
235 <when value="singles">
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
236 <param name="inputs" type="data" label="Concatenate Datasets" multiple="True" format="fastq,fastq.gz,txt,tabular,bed"
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
237 help="All inputed datasets will be concatenated tail-to-head."/>
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
238 </when>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
239 <when value="paired_collection">
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
240 <param name="inputs" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,txt,tabular,bed"
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
241 label="Input paired collection to concatenate"/>
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
242 <param name="paired_cat_type" type="select" label="What type of concatenation do you wish to perform?">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
243 <option value="by_strand">Concatenate all datsets of same strand (outputs a single pair of datasets)</option>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
244 <option value="by_pair">Concatenate pairs of datasets (outputs an unpaired collection of datasets)</option>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
245 <option value="all">Concatenate all datasets into a single file regardless of strand (outputs a single file)</option>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
246 </param>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
247 </when>
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
248 <when value="simple_collections">
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
249 <param name="input_1" type="data_collection" collection_type="list" label="Input first collection" help="The first collection contains the datasets that will be written first in the concatenated file" />
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
250 <param name="input_2" type="data_collection" collection_type="list" label="Input second collection" help="The second collection contains the datasets that will be written last in the concatenated file" />
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
251 </when>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
252 <when value="nested_collection">
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
253 <param name="inputs" type="data_collection" collection_type="list:list" label="Input nested collection" help="The Nested collection which items you want to concatenate." />
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
254 </when>
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
255 </conditional>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
256 <param name="dataset_names" type="boolean" label="Include dataset names?" truevalue="Yes" falsevalue="No" checked="false" help="If 'Yes' is selected '#name of dataset' will be added when concatenating."/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
257 <param name="headers" type="integer" label="Number of lines to skip at the beginning of each concatenation:" value="0" help="This paremeter exists so as to not concatenate comments or headers contained at the start of the files."/>
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
258 </inputs>
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
259 <outputs>
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
260 <data name="out_file1" format_source="inputs" metadata_source="inputs" label="Concatenated datasets">
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
261 <filter>global_condition['input_type'] == 'singles'</filter>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
262 </data>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
263 <data name="paired_out_file" label="${global_condition.inputs.element_identifier}" auto_format="true">
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
264 <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'all'</filter>
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
265 </data>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
266 <collection name="paired_output" type="paired" label="Concatenation by strtand">
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
267 <discover_datasets pattern="(?P&lt;name&gt;.*)\.listed\.(?P&lt;ext&gt;.*)\.listed" format="fastq" visible="false" directory="concatenated"/>
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
268 <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_strand'</filter>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
269 </collection>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
270 <collection name="list_output" type="list" label="Concatenation by pairs">
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
271 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*)\.listed\.(?P&lt;ext&gt;.*)\.listed" format="fastq" visible="false" directory="concatenated"/>
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
272 <filter>(global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_pair') or (global_condition['input_type'] == 'simple_collections') or (global_condition['input_type'] == 'nested_collection')</filter>
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
273 </collection>
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
274 </outputs>
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
275 <tests>
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
276 <!-- Single files concatenation -->
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
277 <test expect_num_outputs="1"> <!-- Test 1 single files concatenation with no other option -->
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
278 <param name="input_type" value="singles" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
279 <param name="inputs" value="1.bed,2.bed"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
280 <param name="dataset_names" value="No" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
281 <param name="headers" value="0" />
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
282 <output name="out_file1" file="cat_wrapper_out1.bed"/>
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
283 </test>
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
284 <test expect_num_outputs="1"> <!-- Test 2 single files concatenation with dataset names activated -->
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
285 <param name="input_type" value="singles" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
286 <param name="inputs" value="1.bed,2.bed"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
287 <param name="dataset_names" value="Yes" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
288 <param name="headers" value="0" />
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
289 <output name="out_file1" file="cat_wrapper_out2.bed"/>
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
290 </test>
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
291 <test expect_num_outputs="1"> <!-- Test 3 single files concatenation skipping 1 line -->
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
292 <param name="input_type" value="singles" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
293 <param name="inputs" value="1.bed,2.bed"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
294 <param name="dataset_names" value="No" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
295 <param name="headers" value="1" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
296 <output name="out_file1" file="cat_wrapper_out3.bed"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
297 </test>
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
298 <test expect_num_outputs="1"> <!-- Test 4 gz handling with no options -->
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
299 <param name="input_type" value="singles" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
300 <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
301 <param name="dataset_names" value="No" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
302 <param name="headers" value="0" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
303 <output name="out_file1" file="1.fastq.gz" decompress="True"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
304 </test>
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
305 <test expect_num_outputs="1"> <!-- Test 5 gz handling with options -->
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
306 <param name="input_type" value="singles" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
307 <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
308 <param name="dataset_names" value="Yes" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
309 <param name="headers" value="4" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
310 <output name="out_file1" file="1_options.fastq.gz" decompress="True"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
311 </test>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
312 <!-- Test paired options -->
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
313 <test expect_num_outputs="1"> <!-- Test 6 paired collection concatenation by_pair with no other option -->
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
314 <param name="input_type" value="paired_collection" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
315 <param name="paired_cat_type" value="by_pair"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
316 <param name="inputs">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
317 <collection type="list:paired">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
318 <element name="2">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
319 <collection type="paired">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
320 <element name="forward" value="2_f.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
321 <element name="reverse" value="2_r.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
322 </collection>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
323 </element>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
324 <element name="3">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
325 <collection type="paired">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
326 <element name="forward" value="3_f.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
327 <element name="reverse" value="3_r.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
328 </collection>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
329 </element>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
330 <element name="4">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
331 <collection type="paired">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
332 <element name="forward" value="4_f.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
333 <element name="reverse" value="4_r.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
334 </collection>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
335 </element>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
336 </collection>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
337 </param>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
338 <param name="dataset_names" value="No" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
339 <param name="headers" value="0" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
340 <output_collection name="list_output" type="list" >
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
341 <element name="2" file="2.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
342 <element name="3" file="3.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
343 <element name="4" file="4.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
344 </output_collection>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
345 </test>
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
346 <test expect_num_outputs="1"> <!-- Test 7 paired collection concatenation by_strand with no other option -->
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
347 <param name="input_type" value="paired_collection" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
348 <param name="paired_cat_type" value="by_strand"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
349 <param name="inputs">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
350 <collection type="list:paired">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
351 <element name="2">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
352 <collection type="paired">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
353 <element name="forward" value="2_f.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
354 <element name="reverse" value="2_r.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
355 </collection>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
356 </element>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
357 <element name="3">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
358 <collection type="paired">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
359 <element name="forward" value="3_f.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
360 <element name="reverse" value="3_r.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
361 </collection>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
362 </element>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
363 <element name="4">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
364 <collection type="paired">
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
365 <element name="forward" value="4_f.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
366 <element name="reverse" value="4_r.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
367 </collection>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
368 </element>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
369 </collection>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
370 </param>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
371 <param name="dataset_names" value="No" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
372 <param name="headers" value="0" />
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
373 <output_collection name="paired_output" type="paired" >
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
374 <element name="forward" file="f.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
375 <element name="reverse" file="r.fastq"/>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
376 </output_collection>
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
377 </test>
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
378 <test expect_num_outputs="1"> <!-- Test 8 - 2 collections concatenation -->
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
379 <param name="input_type" value="simple_collections" />
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
380 <param name="input_1">
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
381 <collection type="list">
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
382 <element name="2" value="2_f.fastq"/>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
383 <element name="3" value="3_f.fastq"/>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
384 <element name="4" value="4_f.fastq"/>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
385 </collection>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
386 </param>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
387 <param name="input_2">
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
388 <collection type="list">
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
389 <element name="2" value="2_r.fastq"/>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
390 <element name="3" value="3_r.fastq"/>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
391 <element name="4" value="4_r.fastq"/>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
392 </collection>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
393 </param>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
394 <param name="dataset_names" value="No" />
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
395 <param name="headers" value="0" />
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
396 <output_collection name="list_output" type="list" count="3" >
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
397 <element name="2" file="2.fastq"/>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
398 <element name="3" file="3.fastq"/>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
399 <element name="4" file="4.fastq"/>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
400 </output_collection>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
401 </test>
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
402 <test expect_num_outputs="1"> <!-- Test 9 - 2 collections concatenation with other options-->
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
403 <param name="input_type" value="simple_collections" />
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
404 <param name="input_1">
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
405 <collection type="list">
7
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
406 <element name="1_f.fastq.gz" value="1_f.fastq.gz"/>
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
407 </collection>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
408 </param>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
409 <param name="input_2">
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
410 <collection type="list">
7
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
411 <element name="1_r.fastq.gz" value="1_r.fastq.gz"/>
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
412 </collection>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
413 </param>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
414 <param name="dataset_names" value="Yes" />
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
415 <param name="headers" value="4" />
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
416 <output_collection name="list_output" type="list" count="1" >
7
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
417 <element name="1_f.fastq.gz_1_r.fastq.gz" file="1_options.fastq.gz" decompress="True"/>
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
418 </output_collection>
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
419 </test>
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
420 <test expect_num_outputs="1"> <!-- Test 10 nested collections concatenation -->
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
421 <param name="input_type" value="nested_collection" />
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
422 <param name="inputs">
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
423 <collection type="list:list">
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
424 <element name="2">
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
425 <collection type="list">
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
426 <element name="2_f" value="2_f.fastq" ftype="fastq"/>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
427 <element name="2_r" value="2_r.fastq" ftype="fastq"/>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
428 </collection>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
429 </element>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
430 <element name="3">
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
431 <collection type="list">
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
432 <element name="3" value="3.fastq" ftype="fastq"/>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
433 </collection>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
434 </element>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
435 </collection>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
436 </param>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
437 <param name="dataset_names" value="No" />
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
438 <param name="headers" value="0" />
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
439 <output_collection name="list_output" type="list" count="2" >
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
440 <element name="2" file="2.fastq"/>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
441 <element name="3" file="3.fastq"/>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
442 </output_collection>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
443 </test>
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
444 <test expect_num_outputs="1"> <!-- Test 11 nested collections concatenation with options and gzip-->
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
445 <param name="input_type" value="nested_collection" />
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
446 <param name="inputs">
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
447 <collection type="list:list">
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
448 <element name="1">
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
449 <collection type="list">
7
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
450 <element name="1_f.fastq.gz" value="1_f.fastq.gz" ftype="fastq.gz"/>
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
451 <element name="1_r.fastq.gz" value="1_r.fastq.gz" ftype="fastq.gz"/>
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
452 </collection>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
453 </element>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
454 </collection>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
455 </param>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
456 <param name="dataset_names" value="Yes" />
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
457 <param name="headers" value="4" />
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
458 <output_collection name="list_output" type="list" count="1" >
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
459 <element name="1" file="1_options.fastq.gz" decompress="True"/>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
460 </output_collection>
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
461 </test>
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
462 </tests>
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
463 <help>
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
464
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
465 .. class:: warningmark
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
466
7
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
467 **WARNINGS:**
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
468
7
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
469 - This tool does not check if the datasets being concatenated are in the same format.
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
470 - When concatenating 2 collections make sure the first collection is the one with the most items.
55cf9d9defd1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
artbio
parents: 6
diff changeset
471 - This tool can't handle nested collection deeper than list:list.
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
472
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
473 -----
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
474
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
475 **What it does**
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
476
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
477 Concatenates datasets and paired collections with multiple options:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
478
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
479 - When the input is a paired collection:
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
480
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
481 - concatenation by strand : forward and reverse datasets are concatenated separately and a list with a single forward - reverse dataset pair is returned
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
482
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
483 - concatenation by pair : forward - reverse dataset pairs are concatenated and a simple dataset collection is returned
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
484
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
485 - whole collection concatenation : all datasets in the collection are concatenated and a single dataset is returned
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
486
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
487 - When the inputs are 2 collections: datasets are concatenated in a pairwise combination and a single dataset collection is returned
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
488
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
489 - When nested collection concatenation: datasets in each sub-collection are concatenated and a simple dataset collection is returned
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
490
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
491 - Skipping lines before concatenation to avoid headers
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
492
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
493 - Add the name of the concatenated files as separator
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
494
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
495 -----
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
496
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
497 **Single datasets concatenation example**
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
498
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
499 Concatenating Dataset::
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
500
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
501 chrX 151087187 151087355 A 0 -
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
502 chrX 151572400 151572481 B 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
503
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
504 with Dataset1::
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
505
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
506 chr1 151242630 151242955 X 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
507 chr1 151271715 151271999 Y 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
508 chr1 151278832 151279227 Z 0 -
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
509
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
510 and with Dataset2::
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
511
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
512 chr2 100000030 200000955 P 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
513 chr2 100000015 200000999 Q 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
514
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
515 will result in the following::
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
516
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
517 chrX 151087187 151087355 A 0 -
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
518 chrX 151572400 151572481 B 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
519 chr1 151242630 151242955 X 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
520 chr1 151271715 151271999 Y 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
521 chr1 151278832 151279227 Z 0 -
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
522 chr2 100000030 200000955 P 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
523 chr2 100000015 200000999 Q 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
524
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
525 -----
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
526
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
527 **2 Collections concatenation**
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
528
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
529 1rst collection::
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
530
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
531 a
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
532 b
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
533 c
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
534 d
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
535
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
536 2nd collection::
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
537
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
538 1
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
539 2
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
540 3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
541 4
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
542
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
543 Concatenation result::
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
544
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
545 A single collection containing:
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
546
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
547 a concatenated with 1
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
548 b concatenated with 2
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
549 c concatenated with 3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
550 d concatenated with 4
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
551
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
552 -----
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
553
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
554 **Paired collection concatenation example**
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
555
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
556 1rst pair::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
557
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
558 forward - reverse
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
559
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
560 2nd pair::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
561
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
562 forward - reverse
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
563
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
564 - Concatenation by strand::
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
565
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
566 concatenates:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
567
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
568 1rst forward + 2nd forward
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
569 1rst reverse + 2nd reverse
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
570
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
571 outputs:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
572
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
573 1 pair
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
574
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
575 - Concatenation by pair::
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
576
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
577 concatenates:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
578
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
579 1rst forward + 1rst reverse
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
580 2nd forward + 2nd reverse
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
581
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
582 outputs:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
583
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
584 2 datasets
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
585
3
62aebaf6cfa0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a
artbio
parents: 2
diff changeset
586 - Concatenate all::
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
587
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
588 concatenates:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
589
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
590 1rst forward + 1rst reverse + 2nd forward + 2nd reverse
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
591
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
592 outputs:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
593
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
594 1 dataset
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
595
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
596 -----
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
597
6
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
598 **Nested collection concatenation example**
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
599
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
600 Nested collection:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
601
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
602 - Experiment
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
603
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
604 - Sample_1
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
605
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
606 - Sample_1_file_1
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
607 - Sample_1_file_2
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
608
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
609 - Sample_2
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
610
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
611 - Sample_2_file_1
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
612 - Sample_2_file_2
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
613 - Sample_2_file_3
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
614
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
615 Concatenation result::
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
616
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
617 A single collection containing:
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
618
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
619 - Sample_1: (Sample_1_file_1 + Sample_1_file_2)
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
620 - Sample_2: (Sample_2_file_1 + Sample_2_file_2 + Sample_2_file_3)
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
621
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
622 -----
4554fa330d3d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4df03fd2d6fbf17a451256c0fb9d30932fc9d637
artbio
parents: 5
diff changeset
623
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
624 **When selecting "Include dataset names" when concatenating files**:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
625
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
626 1rst file name="first_tabular"::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
627
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
628 chrX 151087187 151087355 A 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
629 chrX 151572400 151572481 B 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
630
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
631 2nd file name="second_tabular"::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
632
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
633 chr1 151242630 151242955 X 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
634 chr1 151271715 151271999 Y 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
635 chr1 151278832 151279227 Z 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
636
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
637 output::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
638
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
639 # first_tabular
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
640 chrX 151087187 151087355 A 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
641 chrX 151572400 151572481 B 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
642 # second_tabular
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
643 chr1 151242630 151242955 X 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
644 chr1 151271715 151271999 Y 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
645 chr1 151278832 151279227 Z 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
646
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
647 -----
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
648
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
649 **Skiping lines**
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
650
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
651 1rst file::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
652
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
653 chrX 151087187 151087355 A 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
654 chrX 151572400 151572481 B 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
655
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
656 2nd file::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
657
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
658 chr1 151242630 151242955 X 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
659 chr1 151271715 151271999 Y 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
660 chr1 151278832 151279227 Z 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
661
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
662 skipping 1 line
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
663
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
664 output::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
665
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
666 chrX 151572400 151572481 B 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
667 chr1 151271715 151271999 Y 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
668 chr1 151278832 151279227 Z 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
669
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
670 -----
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
671
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
672 Adapted from galaxy's catWrapper.xml to allow multiple input files.
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
673
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
674 </help>
8
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
675 <citations>
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
676 <citation type="doi">10.1186/gb-2010-11-8-r86</citation>
5b2cc63d7a21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd
artbio
parents: 7
diff changeset
677 </citations>
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
parents:
diff changeset
678 </tool>