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mvdbeekmvdbeek
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Merge pull request #7837 from lldelisle/update_multiqc
Update multiqc
2 parents da91738 + 6b161df commit c8ab9ab

45 files changed

Lines changed: 528 additions & 344 deletions

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‎tools/multiqc/adapterremoval_plugin.xml‎

Lines changed: 10 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -2,16 +2,19 @@
22
<token name="@ADAPTERREMOVAL_COMMAND@"><![CDATA[
33
#set $pattern = "AdapterRemoval ver"
44
#set file_path_list = []
5-
#for $file in $repeat.software_cond.input:
6-
@ESCAPE_IDENTIFIER@
7-
#set file_path = os.path.join($software_dir, str($identifier) + '.settings')
8-
grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
9-
ln -s '$file' '$file_path' &&
10-
#end for
5+
#if str($repeat.software_cond.input) != "None"
6+
#set $at_least_one_input="T"
7+
#for $file in $repeat.software_cond.input:
8+
@ESCAPE_IDENTIFIER@
9+
#set file_path = os.path.join($software_dir, str($identifier) + '.settings')
10+
grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
11+
ln -s '$file' '$file_path' &&
12+
#end for
13+
#end if
1114
]]></token>
1215

1316
<xml name="adapterremoval_form">
14-
<param name="input" type="data" format="txt,tabular" multiple="true" label="Output settings of AdapterRemoval"/>
17+
<param name="input" type="data" format="txt,tabular" multiple="true" label="Output settings of AdapterRemoval" optional="true"/>
1518
</xml>
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<xml name="adapterremoval_test">

‎tools/multiqc/bakta_plugin.xml‎

Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,17 @@
11
<macros>
22
<token name="@BAKTA_COMMAND@"><![CDATA[
33
#set $pattern = "Bakta:"
4-
#for $file in $repeat.software_cond.input
5-
@ESCAPE_IDENTIFIER@
6-
#set file_path = os.path.join($software_dir, str($identifier) + '.txt')
7-
ln -s '$file' '$file_path' &&
8-
#end for
4+
#if str($repeat.software_cond.input) != "None"
5+
#set $at_least_one_input="T"
6+
#for $file in $repeat.software_cond.input
7+
@ESCAPE_IDENTIFIER@
8+
#set file_path = os.path.join($software_dir, str($identifier) + '.txt')
9+
ln -s '$file' '$file_path' &&
10+
#end for
11+
#end if
912
]]></token>
1013
<xml name="bakta_form">
11-
<param name="input" type="data" format="txt" multiple="true" label="Output of Bakta" help="It should contain 'Bakta:'"/>
14+
<param name="input" type="data" format="txt" multiple="true" label="Output of Bakta" help="It should contain 'Bakta:'" optional="true"/>
1215
</xml>
1316
<xml name="bakta_test">
1417
<test expect_num_outputs="3">

‎tools/multiqc/bamtools_plugin.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
@LN_FILES@
55
]]></token>
66
<xml name="bamtools_form">
7-
<param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'This file was produced by bcftools stats'"/>
7+
<param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'This file was produced by bcftools stats'" optional="true"/>
88
</xml>
99
<xml name="bamtools_test">
1010
<test expect_num_outputs="3">

‎tools/multiqc/bbduk_plugin.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
@LN_FILES@
55
]]></token>
66
<xml name="bbduk_form">
7-
<param name="input" type="data" format="txt" multiple="true" label="Output of BBDuk" help="It should contain 'Executing jgi.BBDuk'"/>
7+
<param name="input" type="data" format="txt" multiple="true" label="Output of BBDuk" help="It should contain 'Executing jgi.BBDuk'" optional="true"/>
88
</xml>
99
<xml name="bbduk_test">
1010
<test expect_num_outputs="3">

‎tools/multiqc/bcftools_plugin.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
@LN_FILES@
55
]]></token>
66
<xml name="bcftools_form">
7-
<param name="input" type="data" format="txt" multiple="true" label="Output of BCFtools" help="It should contain 'This file was produced by bcftools stats'"/>
7+
<param name="input" type="data" format="txt" multiple="true" label="Output of BCFtools" help="It should contain 'This file was produced by bcftools stats'" optional="true"/>
88
</xml>
99
<!-- add here your test files and tests, the more stringent the better -->
1010
<xml name="bcftools_test">

‎tools/multiqc/bismark_plugin.xml‎

Lines changed: 41 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -3,35 +3,50 @@
33
#for $j, $repeat2 in enumerate( $repeat.software_cond.output )
44
@CREATE_REPEAT_DIR_1@
55
#if str($repeat2.type) == "align"
6-
#for $file in $repeat2.input
7-
@ESCAPE_IDENTIFIER@
8-
#set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt')
9-
ln -s '$file' '$file_path' &&
10-
#end for
6+
#if str($repeat2.input) != "None"
7+
#set $at_least_one_input="T"
8+
#for $file in $repeat2.input
9+
@ESCAPE_IDENTIFIER@
10+
#set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt')
11+
ln -s '$file' '$file_path' &&
12+
#end for
13+
#end if
1114
#elif str($repeat2.type) == "dedup"
12-
#for $file in $repeat2.input
13-
@ESCAPE_IDENTIFIER@
14-
#set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt')
15-
ln -s '$file' '$file_path' &&
16-
#end for
15+
#if str($repeat2.input) != "None"
16+
#set $at_least_one_input="T"
17+
#for $file in $repeat2.input
18+
@ESCAPE_IDENTIFIER@
19+
#set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt')
20+
ln -s '$file' '$file_path' &&
21+
#end for
22+
#end if
1723
#elif str($repeat2.type) == "meth_extract"
18-
#for $file in $repeat2.input
19-
@ESCAPE_IDENTIFIER@
20-
#set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt')
21-
ln -s '$file' '$file_path' &&
22-
#end for
24+
#if str($repeat2.input) != "None"
25+
#set $at_least_one_input="T"
26+
#for $file in $repeat2.input
27+
@ESCAPE_IDENTIFIER@
28+
#set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt')
29+
ln -s '$file' '$file_path' &&
30+
#end for
31+
#end if
2332
#elif str($repeat2.type) == "m_bias"
24-
#for $file in $repeat2.input
25-
@ESCAPE_IDENTIFIER@
26-
#set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt')
27-
ln -s '$file' '$file_path' &&
28-
#end for
33+
#if str($repeat2.input) != "None"
34+
#set $at_least_one_input="T"
35+
#for $file in $repeat2.input
36+
@ESCAPE_IDENTIFIER@
37+
#set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt')
38+
ln -s '$file' '$file_path' &&
39+
#end for
40+
#end if
2941
#elif str($repeat2.type) == "bam2nuc"
30-
#for $file in $repeat2.input
31-
@ESCAPE_IDENTIFIER@
32-
#set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt')
33-
ln -s '$file' '$file_path' &&
34-
#end for
42+
#if str($repeat2.input) != "None"
43+
#set $at_least_one_input="T"
44+
#for $file in $repeat2.input
45+
@ESCAPE_IDENTIFIER@
46+
#set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt')
47+
ln -s '$file' '$file_path' &&
48+
#end for
49+
#end if
3550
#end if
3651
#end for
3752
]]></token>
@@ -44,7 +59,7 @@
4459
<option value="m_bias">m_bias file</option>
4560
<option value="bam2nuc">bam2nuc file</option>
4661
</param>
47-
<param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
62+
<param name="input" type="data" format="txt" multiple="true" label="Bismark output" optional="true"/>
4863
</repeat>
4964
</xml>
5065
<!-- add here your test files and tests, the more stringent the better -->

‎tools/multiqc/bowtie2_plugin.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
@LN_FILES@
55
]]></token>
66
<xml name="bowtie2_form">
7-
<param name="input" type="data" format="txt" multiple="true" label="Output of Bowtie 2" help="It should contain 'reads; of these:'"/>
7+
<param name="input" type="data" format="txt" multiple="true" label="Output of Bowtie 2" help="It should contain 'reads; of these:'" optional="true"/>
88
</xml>
99
<!-- add here your test files and tests, the more stringent the better -->
1010
<xml name="bowtie2_test">

‎tools/multiqc/busco_plugin.xml‎

Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,17 @@
11
<macros>
22
<token name="@BUSCO_COMMAND@"><![CDATA[
33
## Searches for files "short_summary_[samplename].txt"
4-
#for $file in $repeat.software_cond.input
5-
@ESCAPE_IDENTIFIER@
6-
#set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier))
7-
ln -s '$file' '$file_path' &&
8-
#end for
4+
#if str($repeat.software_cond.input) != "None"
5+
#set $at_least_one_input="T"
6+
#for $file in $repeat.software_cond.input
7+
@ESCAPE_IDENTIFIER@
8+
#set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier))
9+
ln -s '$file' '$file_path' &&
10+
#end for
11+
#end if
912
]]></token>
1013
<xml name="busco_form">
11-
<param name="input" type="data" format="txt" multiple="true" label="Output of BUSCO"/>
14+
<param name="input" type="data" format="txt" multiple="true" label="Output of BUSCO" optional="true"/>
1215
</xml>
1316
<!-- add here your test files and tests, the more stringent the better -->
1417
<xml name="busco_test">

‎tools/multiqc/checkm2_plugin.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
@LN_FILES@
55
]]></token>
66
<xml name="checkm2_form">
7-
<param name="input" type="data" format="tabular" multiple="true" label="Output of CheckM2" help="It should be the quality report from CheckM2"/>
7+
<param name="input" type="data" format="tabular" multiple="true" label="Output of CheckM2" help="It should be the quality report from CheckM2" optional="true"/>
88
</xml>
99
<xml name="checkm2_test">
1010
<test expect_num_outputs="3">

‎tools/multiqc/checkm_plugin.xml‎

Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,17 @@
11
<macros>
22
<token name="@CHECKM_COMMAND@"><![CDATA[
33
#set $pattern = ".*Bin Id(?:\t| {3,})Marker lineage(?:\t| {3,})# genomes(?:\t| {3,})# markers(?:\t| {3,})# marker sets.*"
4-
#for $file in $repeat.software_cond.input
5-
@ESCAPE_IDENTIFIER@
6-
#set file_path = os.path.join($software_dir, 'output_file')
7-
ln -s '$file' '$file_path' &&
8-
#end for
4+
#if str($repeat.software_cond.input) != "None"
5+
#set $at_least_one_input="T"
6+
#for $file in $repeat.software_cond.input
7+
@ESCAPE_IDENTIFIER@
8+
#set file_path = os.path.join($software_dir, 'output_file')
9+
ln -s '$file' '$file_path' &&
10+
#end for
11+
#end if
912
]]></token>
1013
<xml name="checkm_form">
11-
<param name="input" type="data" format="tabular" multiple="true" label="Output of Checkm"/>
14+
<param name="input" type="data" format="tabular" multiple="true" label="Output of Checkm" optional="true"/>
1215
</xml>
1316
<xml name="checkm_test">
1417
<test expect_num_outputs="3">

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